8WV0 | pdb_00008wv0

Outer membrane porin of Burkholderia pseudomallei (BpsOmp38)

• PDB DOI: https://doi.org/10.2210/pdb8WV0/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Burkholderia pseudomallei
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2023-10-22 Released: 2024-10-30 
• Deposition Author(s): Bunkum, P., Aunkham, A., Bert van den, B., Robinson, R.C., Suginta, W.
• Funding Organization(s): Vidyasirimedhi Institute of Science and Technology (VISTEC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.274 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.247 (Depositor), 0.247 (DCC) 
• R-Value Observed: 
  0.249 (Depositor) 

Starting Model: in silico

Literature

Structure and function of outer membrane protein from Burkholderia pseudomallei (BpsOmp38)

Bunkum, P., Aunkham, A., Bert van den, B., Robinson, R.C., Suginta, W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 111.57 kDa 
• Atom Count: 7,421 
• Modeled Residue Count: 992 
• Deposited Residue Count: 1,062 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane porin (Fragment)	A [auth C], B [auth A], C [auth B]	354	Burkholderia pseudomallei	Mutation(s): 0  Gene Names: omp38 Membrane Entity: Yes
UniProt
Find proteins for Q63LY3 (Burkholderia pseudomallei (strain K96243)) Explore Q63LY3  Go to UniProtKB:  Q63LY3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.274 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.247 (Depositor), 0.247 (DCC) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.99	α = 90
b = 98.9	β = 90
c = 147.85	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-30 
Deposition Author(s): Bunkum, P., Aunkham, A., Bert van den, B., Robinson, R.C., Suginta, W.

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Funding Organization	Location	Grant Number
Vidyasirimedhi Institute of Science and Technology (VISTEC)	Thailand	--

Revision History  

• Version 1.0: 2024-10-30
  Type: Initial release