4V6G

Initiation complex of 70S ribosome with two tRNAs and mRNA.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural aspects of messenger RNA reading frame maintenance by the ribosome.

Jenner, L.B.Demeshkina, N.Yusupova, G.Yusupov, M.

(2010) Nat Struct Mol Biol 17: 555-560

  • DOI: 10.1038/nsmb.1790
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • One key question in protein biosynthesis is how the ribosome couples mRNA and tRNA movements to prevent disruption of weak codon-anticodon interactions and loss of the translational reading frame during translocation. Here we report the complete path ...

    One key question in protein biosynthesis is how the ribosome couples mRNA and tRNA movements to prevent disruption of weak codon-anticodon interactions and loss of the translational reading frame during translocation. Here we report the complete path of mRNA on the 70S ribosome at the atomic level (3.1-A resolution), and we show that one of the conformational rearrangements that occurs upon transition from initiation to elongation is a narrowing of the downstream mRNA tunnel. This rearrangement triggers formation of a network of interactions between the mRNA downstream of the A-site codon and the elongating ribosome. Our data elucidate the mechanism by which hypermodified nucleoside 2-methylthio-N6 isopentenyl adenosine at position 37 (ms(2)i(6)A37) in tRNA(Phe)(GAA) stabilizes mRNA-tRNA interactions in all three tRNA binding sites. Another network of contacts is formed between this tRNA modification and ribosomal elements surrounding the mRNA E/P kink, resulting in the anchoring of P-site tRNA. These data allow rationalization of how modification deficiencies of ms(2)i(6)A37 in tRNAs may lead to shifts of the translational reading frame.


    Organizational Affiliation

    Institut de Génétique et de Biologie Moléculaire et Cellulaire, Département de Biologie et de Génomique Structurales, Illkirch, France.



Macromolecules

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S10
AM, CM
105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S11
AN, CN
129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S12
AO, CO
132Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S13
AP, CP
126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S14
AQ, CQ
61Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA1679
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Find proteins for P24320 (Thermus thermophilus)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S15
AR, CR
89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S16
AS, CS
88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S17
AT, CT
105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
Find proteins for P0DOY7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S18
AU, CU
88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S19
AV, CV
93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S2
AE, CE
256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S20
AW, CW
106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN THX
AX, CX
27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
BD, DD
276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
Find proteins for P60405 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
BE, DE
206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
Find proteins for Q5SHN8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
BF, DF
210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
Find proteins for Q5SHN9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
BG, DG
182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
Find proteins for Q5SHQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S3
AF, CF
239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
BH, DH
180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplFTTHA1677
Find proteins for P0DOY8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
BK, DK
148Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplITTHA0242
Find proteins for Q5SLQ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
BM, DM
140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
Find proteins for P60488 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
BN, DN
122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
Find proteins for Q5SHP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
BO, DO
150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
Find proteins for Q5SHQ7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
BP, DP
141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
Find proteins for P60489 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
B0, D0
118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
Find proteins for Q9Z9H5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
BQ, DQ
112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
Find proteins for Q5SHQ4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
BR, DR
146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
Find proteins for P60490 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
B1, D1
118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
Find proteins for P60491 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S4
AG, CG
209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
B2, D2
101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
Find proteins for P60492 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60492

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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
BS, DS
113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
Find proteins for Q5SHP3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP3

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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
BT, DT
96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
Find proteins for Q5SHP0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
BU, DU
110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
Find proteins for Q5SHP9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
BV, DV
206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
Find proteins for Q5SHZ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
B3, D3
85Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
Find proteins for P60493 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
BZ, DZ
98Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
Find proteins for P60494 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
BW, DW
72Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
Find proteins for Q5SHP6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
BX, DX
60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
Find proteins for Q5SHQ6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
B4, D4
71Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
Find proteins for Q5SJE1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S5
AH, CH
162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
B5, D5
60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
Find proteins for P80339 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
B6, D6
54Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
Find proteins for P35871 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
B7, D7
49Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
Find proteins for P80340 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
B8, D8
65Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
Find proteins for Q5SKU1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S6
AI, CI
101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S7
AJ, CJ
156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S8
AK, CK
138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S9
AL, CL
128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 1
MoleculeChainsLengthOrganism
16S RRNA (E.COLI NUMBERING)AA, CA1517Thermus thermophilus HB8

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Entity ID: 22
MoleculeChainsLengthOrganism
TRNA FMET (UNMODIFIED BASES)AC, AD,CB,CC,CD77Escherichia coli

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Entity ID: 23
MoleculeChainsLengthOrganism
MRNAA1, C125synthetic construct

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Entity ID: 24
MoleculeChainsLengthOrganism
23S ribosomal RNABA, DA2898Thermus thermophilus HB8

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Entity ID: 25
MoleculeChainsLengthOrganism
5S ribosomal RNABB, DB122Thermus thermophilus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
AA, AG, AQ, CG, CQ
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A1, AA, AC, AD, AH, AI, AJ, AK, AL, AO, AP, AQ, AS, AT, AW, AX, B0, B1, B3, B4, B5, B6, B8, BA, BB, BD, BE, BF, BG, BH, BK, BO, BQ, BR, BT, BU, BW, BZ, C1, CA, CC, CD, CG, CH, CK, CL, CM, CP, CQ, CR, CS, CT, CW, CX, D0, D1, D2, D3, D5, D6, D7, DA, DB, DD, DE, DF, DG, DH, DO, DR, DS, DT, DU, DW, DZ
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.46α = 90
b = 452.18β = 90
c = 626.12γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction
XSCALEdata 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