4DSD

Crystal structure of a putative periplasmic protein (BACOVA_05534) from Bacteroides ovatus ATCC 8483 at 1.75 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4DSD/pdb

• Classification: Structural Genomics, Unknown Function
• Organism(s): Bacteroides ovatus ATCC 8483
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-02-18 Released: 2012-03-21 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.214 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Crystal structure of a putative periplasmic protein (BACOVA_05534) from Bacteroides ovatus ATCC 8483 at 1.75 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 2  

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

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

Macromolecule Content

• Total Structure Weight: 30.09 kDa 
• Atom Count: 2,365 
• Modelled Residue Count: 252 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative periplasmic protein	A, B	129	Bacteroides ovatus ATCC 8483	Mutation(s): 0  Gene Names: BACOVA_05534

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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: 1.75 Å
• R-Value Free:  0.214 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34DSD

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.381	α = 90
b = 107.381	β = 90
c = 63.01	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: 2012-03-21 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2012-03-21
  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: 2024-11-20
  Changes: Data collection, Structure summary