3U6G

Crystal structure of a domain of unknown function, DUF4425 (BVU_3708) from Bacteroides vulgatus ATCC 8482 at 1.35 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3U6G/pdb

• Classification: Structural Genomics, Unknown Function
• Organism(s): Phocaeicola vulgatus ATCC 8482
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-10-12 Released: 2011-11-02 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.207 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 

Literature

Crystal structure of a domain of unknown function, DUF4425 (BVU_3708) from Bacteroides vulgatus ATCC 8482 at 1.35 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 27.16 kDa 
• Atom Count: 2,256 
• Modelled Residue Count: 248 
• Deposited Residue Count: 252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein DUF4425	A, B	126	Phocaeicola vulgatus ATCC 8482	Mutation(s): 0  Gene Names: BVU_3708
UniProt
Find proteins for A6L6K5 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154)) Explore A6L6K5  Go to UniProtKB:  A6L6K5

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.207 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 
• Space Group: P 2₁ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M33U6G

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.237	α = 90
b = 99.302	β = 90
c = 41.085	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-02 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2011-11-02
  Type: Initial release
  
• Version 1.1: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-02-01
  Changes: Database references, Derived calculations