1WPB | pdb_00001wpb

Structure of Escherichia coli yfbU gene product

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.227 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.190 (Depositor) 
  • R-Value Observed: 
    0.190 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1WPB

This is version 1.3 of the entry. See complete history. 

Literature

Crystal structure of Escherichia coli yfbU gene product

Borek, D., Chen, Y., Zheng, M., Skarina, T., Savchenko, A., Edwards, A., Otwinowski, Z.

To be published.

Macromolecule Content 

  • Total Structure Weight: 332.45 kDa 
  • Atom Count: 24,406 
  • Modeled Residue Count: 2,687 
  • Deposited Residue Count: 2,752 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
hypothetical protein yfbU
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
172Escherichia coliMutation(s): 0 
Gene Names: yfbU
UniProt
Find proteins for Q1R9C1 (Escherichia coli (strain UTI89 / UPEC))
Explore Q1R9C1 
Go to UniProtKB:  Q1R9C1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1R9C1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL


Download:Ideal Coordinates CCD File
AC [auth L]
DB [auth H]
DC [auth M]
EA [auth C]
EB [auth H]
AC [auth L],
DB [auth H],
DC [auth M],
EA [auth C],
EB [auth H],
EC [auth M],
FA [auth C],
FB [auth H],
FC [auth M],
HC [auth N],
IC [auth N],
JA [auth D],
JC [auth N],
KA [auth D],
KB [auth I],
KC [auth N],
LA [auth D],
LB [auth I],
MA [auth D],
NC [auth O],
OC [auth O],
PA [auth E],
PB [auth J],
QA [auth E],
QB [auth J],
QC [auth P],
R [auth A],
RA [auth E],
RC [auth P],
S [auth A],
SA [auth E],
TB [auth K],
U [auth B],
UB [auth K],
V [auth B],
VB [auth K],
W [auth B],
WA [auth F],
WB [auth K],
X [auth B],
Y [auth B],
YA [auth G],
ZA [auth G],
ZB [auth L]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL


Download:Ideal Coordinates CCD File
AA [auth C]
AB [auth H]
BA [auth C]
BB [auth H]
BC [auth M]
AA [auth C],
AB [auth H],
BA [auth C],
BB [auth H],
BC [auth M],
CA [auth C],
CB [auth H],
CC [auth M],
DA [auth C],
GA [auth D],
GB [auth I],
GC [auth N],
HA [auth D],
HB [auth I],
IA [auth D],
IB [auth I],
JB [auth I],
LC [auth O],
MB [auth J],
MC [auth O],
NA [auth E],
NB [auth J],
OA [auth E],
OB [auth J],
PC [auth P],
Q [auth A],
RB [auth K],
SB [auth K],
T [auth B],
TA [auth F],
UA [auth F],
VA [auth F],
XA [auth G],
XB [auth L],
YB [auth L],
Z [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.227 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.190 (Depositor) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 230.521α = 90
b = 230.521β = 90
c = 230.521γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
REFMACrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-12-25
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary