6WN8 | pdb_00006wn8

2.70 Angstrom Resolution Crystal Structure of Uracil Phosphoribosyl Transferase from Klebsiella pneumoniae

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.219 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history. 


Literature

A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae.

Inniss, N.L., Kochan, T.J., Minasov, G., Wawrzak, Z., Chang, C., Tan, K., Shuvalova, L., Kiryukhina, O., Pshenychnyi, S., Wu, R., Dubrovska, I., Babnigg, G., Endres, M., Anderson, W.F., Hauser, A.R., Joachimiak, A., Satchell, K.J.F.

(2023) Microbiol Resour Announc 12: e0101322-e0101322

  • DOI: https://doi.org/10.1128/mra.01013-22
  • Primary Citation of Related Structures:  
    6DT3, 6DUX, 6DVV, 6DXN, 6E85, 6NAU, 6NBG, 6NDI, 6WN5, 6WN8, 6X1L, 7RJJ, 7TL5, 7TZP

  • PubMed Abstract: 

    Klebsiella pneumoniae is a leading cause of antibiotic-resistant-associated deaths in the world. Here, we report the deposition of 14 structures of enzymes from both the core and accessory genomes of sequence type 23 (ST23) K1 hypervirulent K. pneumoniae.

    • Organizational Affiliation: 
    • Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uracil phosphoribosyltransferase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
211Klebsiella pneumoniae subsp. pneumoniaeMutation(s): 0 
Gene Names: 
EC: 2.4.2.9
UniProt
Find proteins for A6TCB0 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578))
Explore A6TCB0 
Go to UniProtKB:  A6TCB0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6TCB0
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
K
2N/A
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BDF
Query on BDF
Download Ideal Coordinates CCD File 
AA [auth B],
JB [auth E],
KB [auth E],
L [auth A],
M [auth A]		beta-D-fructopyranose
C6 H12 O6
LKDRXBCSQODPBY-ARQDHWQXSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
AB [auth D]
AC [auth F]
AD [auth H]
BA [auth B]
BB [auth D]
AB [auth D],
AC [auth F],
AD [auth H],
BA [auth B],
BB [auth D],
BC [auth F],
BD [auth H],
CA [auth B],
CB [auth D],
CC [auth F],
CD [auth H],
DA [auth B],
DB [auth D],
DC [auth F],
DD [auth I],
EA [auth B],
EB [auth D],
ED [auth I],
FA [auth B],
FB [auth D],
FD [auth I],
GA [auth B],
GB [auth D],
GD [auth I],
HA [auth B],
HB [auth D],
HD [auth I],
IA [auth B],
IC [auth G],
ID [auth I],
JC [auth G],
JD [auth I],
KC [auth G],
KD [auth I],
LA [auth C],
LB [auth E],
LC [auth G],
LD [auth I],
MA [auth C],
MB [auth E],
MC [auth G],
N [auth A],
NA [auth C],
NB [auth E],
NC [auth G],
O [auth A],
OA [auth C],
OB [auth E],
OC [auth G],
OD [auth J],
P [auth A],
PA [auth C],
PB [auth E],
PC [auth G],
PD [auth J],
Q [auth A],
QA [auth C],
QB [auth E],
QD [auth J],
R [auth A],
RA [auth C],
RB [auth E],
RC [auth H],
RD [auth J],
S [auth A],
SA [auth C],
SC [auth H],
SD [auth J],
T [auth A],
TA [auth C],
TC [auth H],
TD [auth J],
U [auth A],
UA [auth C],
UC [auth H],
UD [auth J],
V [auth A],
VA [auth C],
VB [auth F],
VC [auth H],
WB [auth F],
WC [auth H],
XA [auth D],
XB [auth F],
XC [auth H],
YA [auth D],
YB [auth F],
YC [auth H],
ZA [auth D],
ZB [auth F],
ZC [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL
Download Ideal Coordinates CCD File 
EC [auth F]
FC [auth F]
GC [auth F]
HC [auth F]
IB [auth D]
EC [auth F],
FC [auth F],
GC [auth F],
HC [auth F],
IB [auth D],
JA [auth B],
KA [auth B],
MD [auth I],
ND [auth I],
QC [auth G],
SB [auth E],
TB [auth E],
UB [auth E],
VD [auth J],
W [auth A],
WA [auth C],
WD [auth J],
X [auth A],
XD [auth J],
Y [auth A],
YD [auth J],
Z [auth A],
ZD [auth J]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 203.349α = 90
b = 203.349β = 90
c = 157.775γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-06
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-06-14
    Changes: Database references, Structure summary
  • Version 2.2: 2023-10-25
    Changes: Data collection, Refinement description