4ZGF | pdb_00004zgf

Crystal structure of a duf4847 family protein (BVU_2626) from Bacteroides vulgatus ATCC 8482 at 1.00 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 
    0.137 (Depositor), 0.138 (DCC) 
  • R-Value Work: 
    0.116 (Depositor), 0.118 (DCC) 
  • R-Value Observed: 
    0.117 (Depositor) 

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a duf4847 family protein (BVU_2626) from Bacteroides vulgatus ATCC 8482 at 1.00 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content 

  • Total Structure Weight: 17.27 kDa 
  • Atom Count: 1,655 
  • Modeled Residue Count: 141 
  • Deposited Residue Count: 141 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Uncharacterized protein141Phocaeicola vulgatus ATCC 8482Mutation(s): 0 
Gene Names: BVU_2626
UniProt
Find proteins for A6L3L5 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154))
Explore A6L3L5 
Go to UniProtKB:  A6L3L5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6L3L5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P6G

Query on P6G


Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A],
H [auth A]		HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
BEZ

Query on BEZ


Download:Ideal Coordinates CCD File
K [auth A]BENZOIC ACID
C7 H6 O2
WPYMKLBDIGXBTP-UHFFFAOYSA-N
ACT

Query on ACT


Download:Ideal Coordinates CCD File
I [auth A],
J [auth A]		ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA

Query on CA


Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free:  0.137 (Depositor), 0.138 (DCC) 
  • R-Value Work:  0.116 (Depositor), 0.118 (DCC) 
  • R-Value Observed: 0.117 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.747α = 90
b = 55.486β = 90
c = 76.176γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
REFMACrefinement
SHELXDphasing
XDSdata reduction

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: 2015-05-06
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Advisory, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.2: 2023-02-01
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-10-23
    Changes: Data collection, Structure summary