4QFU

Crystal structure of a glycoside hydrolase family 5 (BVU_2644) from Bacteroides vulgatus ATCC 8482 at 1.90 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of a glycoside hydrolase family 5 (BVU_2644) from Bacteroides vulgatus ATCC 8482 at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
glycoside hydrolase family 5
A, B, C, D, E, F, G, H, I, J, K, L
A, B, C, D, E, F, G, H, I, J, K, L
484Phocaeicola vulgatus ATCC 8482Mutation(s): 0 
Gene Names: BVU_2644
UniProt
Find proteins for A6L3N2 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154))
Explore A6L3N2 
Go to UniProtKB:  A6L3N2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6L3N2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MRD
Query on MRD

Download Ideal Coordinates CCD File 
AA [auth E],
AB [auth L],
BA [auth E],
EA [auth F],
FA [auth F],
AA [auth E],
AB [auth L],
BA [auth E],
EA [auth F],
FA [auth F],
IA [auth G],
JA [auth G],
M [auth A],
MA [auth H],
N [auth A],
NA [auth H],
P [auth B],
PA [auth I],
Q [auth B],
QA [auth I],
SA [auth J],
T [auth C],
TA [auth J],
VA [auth K],
W [auth D],
WA [auth K],
X [auth D],
Z [auth E],
ZA [auth L]
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
SAR
Query on SAR

Download Ideal Coordinates CCD File 
KA [auth G],
U [auth C],
XA [auth K]
SARCOSINE
C3 H7 N O2
FSYKKLYZXJSNPZ-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

Download Ideal Coordinates CCD File 
CA [auth E],
GA [auth F],
R [auth B]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
BB [auth L],
DA [auth E],
HA [auth F],
LA [auth G],
O [auth A],
BB [auth L],
DA [auth E],
HA [auth F],
LA [auth G],
O [auth A],
OA [auth H],
RA [auth I],
S [auth B],
UA [auth J],
V [auth C],
Y [auth D],
YA [auth K]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H, I, J, K, L
A, B, C, D, E, F, G, H, I, J, K, L
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 
  • Space Group: P 1
  • Diffraction Data DOI: 10.18430/M34QFU Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.95α = 91.6
b = 117.589β = 92.82
c = 125.249γ = 98.92
Software Package:
Software NamePurpose
MolProbitymodel building
PDB_EXTRACTdata extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
BUSTER-TNTrefinement
PHASERphasing
XDSdata reduction
SHELXDphasing
autoSHARPphasing
BUSTERrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2018-01-24
    Changes: Database references