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), 0.217 (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 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.

Macromolecule Content 

  • Total Structure Weight: 239.47 kDa 
  • Atom Count: 16,930 
  • Modeled Residue Count: 2,087 
  • Deposited Residue Count: 2,110 
  • Unique protein chains: 1

Macromolecules

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|  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

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD 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), 0.217 (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