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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.274 (Depositor), 0.276 (DCC)
R-Value Work:
0.247 (Depositor), 0.248 (DCC)
R-Value Observed:
0.249 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q63LY3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.274 (Depositor), 0.276 (DCC)
R-Value Work: 0.247 (Depositor), 0.248 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-10-30

Deposition Author(s):

Bert van den, B.

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.