3D33 | pdb_00003d33

Crystal structure of a duf3244 family protein with an immunoglobulin-like beta-sandwich fold (bvu_0276) from bacteroides vulgatus atcc 8482 at 1.70 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3D33/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Phocaeicola vulgatus ATCC 8482
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-09 Released: 2008-05-27 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Crystal structure of Domain of Unknown Function with an Immunoglobulin-like Beta-sandwich Fold (YP_001297618.1) from Bacteroides vulgatus ATCC 8482 at 1.70 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 23.9 kDa 
• Atom Count: 1,775 
• Modeled Residue Count: 187 
• Deposited Residue Count: 216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Domain of Unknown Function with an Immunoglobulin-like Beta-sandwich Fold	A, B	108	Phocaeicola vulgatus ATCC 8482	Mutation(s): 0  Gene Names: YP_001297618.1, BVU_0276
UniProt
Find proteins for A6KX32 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154)) Explore A6KX32  Go to UniProtKB:  A6KX32

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: 1.70 Å
• R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33D33

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.562	α = 90
b = 55.179	β = 94.31
c = 47.116	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-27 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-05-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references
• Version 1.5: 2024-11-20
  Changes: Data collection, Refinement description, Structure summary