3DXI | pdb_00003dxi

Crystal structure of the N-terminal domain of a putative aldolase (BVU_2661) from Bacteroides vulgatus

• PDB DOI: https://doi.org/10.2210/pdb3DXI/pdb

• Classification: structural genomics, unknown function
• Organism(s): Phocaeicola vulgatus ATCC 8482
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-24 Released: 2008-08-26 
• Deposition Author(s): Eswaramoorthy, S., Pabalan, A.A., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Literature

Crystal structure of the N-terminal domain of a putative aldolase (BVU_2661) from Bacteroides vulgatus

Eswaramoorthy, S., Pabalan, A.A., Burley, S.K., Swaminathan, S.

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)

Macromolecule Content 

• Total Structure Weight: 74.22 kDa 
• Atom Count: 5,201 
• Modeled Residue Count: 598 
• Deposited Residue Count: 640 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative aldolase	A, B	320	Phocaeicola vulgatus ATCC 8482	Mutation(s): 0  Gene Names: BVU_2661
UniProt
Find proteins for A6L3P9 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154)) Explore A6L3P9  Go to UniProtKB:  A6L3P9

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: 2.04 Å
• R-Value Free:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.258	α = 90
b = 65.639	β = 90
c = 177.835	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELX	model building
CNS	refinement
DENZO	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-26 
Deposition Author(s): Eswaramoorthy, S., Pabalan, A.A., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-08-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Structure summary