3LUB

Crystal structure of Putative creatinine amidohydrolase (YP_211512.1) from Bacteroides fragilis NCTC 9343 at 2.11 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structure of Putative creatinine amidohydrolase (YP_211512.1) from Bacteroides fragilis NCTC 9343 at 2.11 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative creatinine amidohydrolase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
254Bacteroides fragilis NCTC 9343Mutation(s): 0 
Gene Names: BF1877
UniProt
Find proteins for Q5LE76 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / NCTC 9343 / Onslow))
Explore Q5LE76 
Go to UniProtKB:  Q5LE76
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5LE76
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth D]
AB [auth I]
BA [auth D]
BB [auth I]
FB [auth J]
AA [auth D],
AB [auth I],
BA [auth D],
BB [auth I],
FB [auth J],
GB [auth J],
HA [auth E],
IA [auth E],
KB [auth K],
LB [auth K],
M [auth A],
N [auth A],
OA [auth F],
PA [auth F],
PB [auth L],
Q [auth B],
QB [auth L],
R [auth B],
SA [auth G],
TA [auth G],
U [auth C],
V [auth C],
XA [auth H],
YA [auth H]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
EA [auth D]
FA [auth D]
IB [auth J]
LA [auth E]
MB [auth K]
EA [auth D],
FA [auth D],
IB [auth J],
LA [auth E],
MB [auth K],
NB [auth K],
S [auth B],
SB [auth L],
VA [auth G],
X [auth C],
Y [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
CA [auth D]
CB [auth I]
DA [auth D]
DB [auth I]
HB [auth J]
CA [auth D],
CB [auth I],
DA [auth D],
DB [auth I],
HB [auth J],
JA [auth E],
KA [auth E],
O [auth A],
QA [auth F],
RB [auth L],
UA [auth G],
W [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
EB [auth I]
GA [auth D]
JB [auth J]
MA [auth E]
NA [auth E]
EB [auth I],
GA [auth D],
JB [auth J],
MA [auth E],
NA [auth E],
OB [auth K],
P [auth A],
RA [auth F],
T [auth B],
TB [auth L],
WA [auth G],
Z [auth C],
ZA [auth H]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.906α = 90
b = 156.79β = 95.29
c = 170.161γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2019-07-17
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2023-02-01
    Changes: Database references, Derived calculations