4V4I

Crystal Structure of a 70S Ribosome-tRNA Complex Reveals Functional Interactions and Rearrangements.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.71 Å
  • R-Value Free: 0.353 
  • R-Value Work: 0.348 
  • R-Value Observed: 0.349 

wwPDB Validation 3D Report Full Report



Literature

Crystal Structure of a 70S Ribosome-tRNA Complex Reveals Functional Interactions and Rearrangements

Korostelev, A.Trakhanov, S.Laurberg, M.Noller, H.F.

(2006) Cell 126: 1065-1077

  • DOI: 10.1016/j.cell.2006.08.032
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Our understanding of the mechanism of protein synthesis has undergone rapid progress in recent years as a result of low-resolution X-ray and cryo-EM structures of ribosome functional complexes and high-resolution structures of ribosomal subunits and ...

    Our understanding of the mechanism of protein synthesis has undergone rapid progress in recent years as a result of low-resolution X-ray and cryo-EM structures of ribosome functional complexes and high-resolution structures of ribosomal subunits and vacant ribosomes. Here, we present the crystal structure of the Thermus thermophilus 70S ribosome containing a model mRNA and two tRNAs at 3.7 A resolution. Many structural details of the interactions between the ribosome, tRNA, and mRNA in the P and E sites and the ways in which tRNA structure is distorted by its interactions with the ribosome are seen. Differences between the conformations of vacant and tRNA-bound 70S ribosomes suggest an induced fit of the ribosome structure in response to tRNA binding, including significant changes in the peptidyl-transferase catalytic site.


    Organizational Affiliation

    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
C
206Thermus thermophilusMutation(s): 0 
Gene Names: rplCTT_C1328
Find proteins for Q72I04 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I04

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
L
118Thermus thermophilusMutation(s): 0 
Gene Names: rplQTT_C1299
Find proteins for Q72I33 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I33

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
M
112Thermus thermophilusMutation(s): 0 
Gene Names: rplRTT_C1312
Find proteins for Q72I20 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I20

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
O
118Thermus thermophilusMutation(s): 0 
Gene Names: rplTTT_C0185
Find proteins for Q72L76 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72L76

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
Q
113Thermus thermophilusMutation(s): 0 
Gene Names: rplVTT_C1323
Find proteins for Q72I09 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I09

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
R
96Thermus thermophilusMutation(s): 0 
Gene Names: rplWTT_C1326
Find proteins for Q72I06 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I06

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
W
72Thermus thermophilusMutation(s): 0 
Gene Names: rpmCTT_C1320
Find proteins for Q72I12 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I12

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
X
60Thermus thermophilusMutation(s): 0 
Gene Names: rpmDTT_C1310
Find proteins for Q72I22 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I22

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
Y
60Thermus thermophilusMutation(s): 0 
Gene Names: rpmFrpl32TT_C0050
Find proteins for P62652 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62652

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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
a
65Thermus thermophilusMutation(s): 0 
Gene Names: rpmITT_C0184
Find proteins for Q72L77 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72L77

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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
b
37Thermus thermophilusMutation(s): 0 
Gene Names: rpmJTT_C1304
Find proteins for Q72I28 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I28

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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
d
239Thermus thermophilusMutation(s): 0 
Gene Names: rpsCrps3TT_C1322
Find proteins for P62663 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62663

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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
h
156Thermus thermophilusMutation(s): 0 
Gene Names: rpsGrps7TT_C1332
Find proteins for P62667 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62667

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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
i
138Thermus thermophilusMutation(s): 0 
Gene Names: rpsHrps8TT_C1314
Find proteins for P62668 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62668

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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
k
105Thermus thermophilusMutation(s): 0 
Gene Names: rpsJrps10TT_C1329
Find proteins for P62653 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62653

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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
m
132Thermus thermophilusMutation(s): 0 
Gene Names: rpsLrps12TT_C1333
Find proteins for P61941 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P61941

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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
n
126Thermus thermophilusMutation(s): 0 
Gene Names: rpsMrps13TT_C1303
Find proteins for P62655 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62655

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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
o
61Thermus thermophilusMutation(s): 0 
Gene Names: rpsZrps14rpsNTT_C1315
Find proteins for P62656 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62656

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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
t
93Thermus thermophilusMutation(s): 0 
Gene Names: rpsSrps19TT_C1324
Find proteins for P62660 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62660

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
H
163Thermus thermophilusMutation(s): 0 
Gene Names: rplMTT_C1101
Find proteins for Q72IN1 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72IN1

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
I
122Thermus thermophilusMutation(s): 0 
Gene Names: rplNTT_C1318
Find proteins for Q72I14 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I14

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
J
150Thermus thermophilusMutation(s): 0 
Gene Names: rplOTT_C1309
Find proteins for Q72I23 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I23

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
K
141Thermus thermophilusMutation(s): 0 
Gene Names: rplPTT_C1321
Find proteins for Q72I11 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I11

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
N
146Thermus thermophilusMutation(s): 0 
Gene Names: rplSTT_C0669
Find proteins for Q72JU9 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72JU9

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
P
101Thermus thermophilusMutation(s): 0 
Gene Names: rplUTT_C1424
Find proteins for Q72HR2 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72HR2

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
S
110Thermus thermophilusMutation(s): 0 
Gene Names: rplXTT_C1317
Find proteins for Q72I15 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I15

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
T
206Thermus thermophilusMutation(s): 0 
Gene Names: rplYctcTT_C1225
Find proteins for Q72IA7 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72IA7

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
U
85Thermus thermophilusMutation(s): 0 
Gene Names: rpmATT_C1423
Find proteins for Q72HR3 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72HR3

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
V
98Thermus thermophilusMutation(s): 0 
Gene Names: rpmBTT_C1964
Find proteins for Q72G84 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72G84

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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
Z
49Thermus thermophilusMutation(s): 0 
Find proteins for P80340 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80340

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
A
229Thermus thermophilusMutation(s): 0 
Gene Names: rplATT_C1739
Find proteins for Q72GV9 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72GV9

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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
c
256Thermus thermophilusMutation(s): 0 
Gene Names: rpsBrps2TT_C0509
Find proteins for P62662 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62662

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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
e
209Thermus thermophilusMutation(s): 0 
Gene Names: rpsDrps4TT_C1301
Find proteins for P62664 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62664

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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
f
162Thermus thermophilusMutation(s): 0 
Gene Names: rpsErps5TT_C1311
Find proteins for P62665 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62665

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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
g
101Thermus thermophilusMutation(s): 0 
Gene Names: rpsFrps6TT_C1740
Find proteins for P62666 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62666

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
B
276Thermus thermophilusMutation(s): 0 
Gene Names: rplBTT_C1325
Find proteins for Q72I07 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I07

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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
j
128Thermus thermophilusMutation(s): 0 
Gene Names: rpsIrps9TT_C1100
Find proteins for P62669 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62669

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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
l
129Thermus thermophilusMutation(s): 0 
Gene Names: rpsKrps11TT_C1302
Find proteins for P62654 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62654

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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
p
89Thermus thermophilusMutation(s): 0 
Gene Names: rpsOrps15TT_C0773
Find proteins for P62657 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62657

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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
q
88Thermus thermophilusMutation(s): 0 
Gene Names: rpsPrps16TT_C0673
Find proteins for P62238 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62238

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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
r
105Thermus thermophilusMutation(s): 0 
Gene Names: rpsQrps17TT_C1319
Find proteins for P62658 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62658

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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
s
88Thermus thermophilusMutation(s): 0 
Gene Names: rpsRrps18TT_C1742
Find proteins for P62659 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62659

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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
u
106Thermus thermophilusMutation(s): 0 
Gene Names: rpsTrps20TT_C1031
Find proteins for P62661 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62661

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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx
v
27Thermus thermophilusMutation(s): 0 
Gene Names: rpsUTT_C1030
Find proteins for P62613 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62613

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
D
205Thermus thermophilusMutation(s): 0 
Gene Names: rplDTT_C1327
Find proteins for Q72I05 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I05

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
E
182Thermus thermophilusMutation(s): 0 
Gene Names: rplETT_C1316
Find proteins for Q72I16 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I16

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
F
180Thermus thermophilusMutation(s): 0 
Gene Names: rplFTT_C1313
Find proteins for Q72I19 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I19

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
G
148Thermus thermophilusMutation(s): 0 
Gene Names: rplITT_C1743
Find proteins for Q72GV5 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72GV5

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Entity ID: 31
MoleculeChainsLengthOrganism
16S SMALL SUBUNIT RIBOSOMAL RNAy1522Thermus thermophilus

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Entity ID: 32
MoleculeChainsLengthOrganism
P-site PHE-tRNAz76Escherichia coli
Entity ID: 34
MoleculeChainsLengthOrganism
MRNA110N/A

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Entity ID: 1
MoleculeChainsLengthOrganism
23S LARGE SUBUNIT RIBOSOMAL RNAw2889Thermus thermophilus

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Entity ID: 2
MoleculeChainsLengthOrganism
5S LARGE SUBUNIT RIBOSOMAL RNAx121Thermus thermophilus

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Entity ID: 33
MoleculeChainsLengthOrganism
E-TRNA076Thermus thermophilus
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.71 Å
  • R-Value Free: 0.353 
  • R-Value Work: 0.348 
  • R-Value Observed: 0.349 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 507.81α = 90
b = 507.81β = 90
c = 689.52γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
CNSrefinement
d*TREKdata reduction
CCP4data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 2.0: 2019-07-03
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary