3ORJ | pdb_00003orj

Crystal structure of a sugar-binding protein (BACOVA_04391) from Bacteroides ovatus at 2.16 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3ORJ/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Bacteroides ovatus ATCC 8483
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-09-07 Released: 2010-10-13 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 
  0.229 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

Crystal structure of a sugar-binding protein (BACOVA_04391) from Bacteroides ovatus at 2.16 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, light scattering

Macromolecule Content 

• Total Structure Weight: 48.49 kDa 
• Atom Count: 3,578 
• Modeled Residue Count: 429 
• Deposited Residue Count: 439 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
sugar-binding protein	A	439	Bacteroides ovatus ATCC 8483	Mutation(s): 0  Gene Names: BACOVA_04391

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 2.16 Å
• R-Value Free:  0.229 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33ORJ

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.456	α = 90
b = 71.962	β = 90
c = 120.806	γ = 90

Software Package:

Software Name	Purpose
SHELX	phasing
BUSTER-TNT	refinement
XSCALE	data processing
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
SHELXD	phasing
autoSHARP	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-13 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-07-20
  Changes: Structure summary
• Version 1.3: 2017-10-25
  Changes: Author supporting evidence
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Structure summary