4F7A | pdb_00004f7a

Crystal structure of a susd homolog (BVU_2203) from Bacteroides vulgatus ATCC 8482 at 1.85 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4F7A/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Phocaeicola vulgatus ATCC 8482
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-05-15 Released: 2012-05-30 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.162 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Literature

Crystal structure of a susd homolog (BVU_2203) from Bacteroides vulgatus ATCC 8482 at 1.85 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.

Macromolecule Content 

• Total Structure Weight: 58.32 kDa 
• Atom Count: 4,580 
• Modeled Residue Count: 498 
• Deposited Residue Count: 511 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A	511	Phocaeicola vulgatus ATCC 8482	Mutation(s): 0  Gene Names: BVU_2203
UniProt
Find proteins for A6L2F0 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154)) Explore A6L2F0  Go to UniProtKB:  A6L2F0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	D [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.162 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34F7A

Space Group: P 4₃ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.379	α = 90
b = 160.379	β = 90
c = 160.379	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-30 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2012-05-30
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.4: 2024-11-27
  Changes: Data collection, Structure summary