8XNB | pdb_00008xnb

Cryo-EM structure of Deinococcus radiodurans BamA

PDB DOI: https://doi.org/10.2210/pdb8XNB/pdb
EM Map EMD-38500: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2023-12-29 Released: 2025-01-15
Deposition Author(s): Qian, H.W., Wang, Z.Z.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8XNB

This is version 1.2 of the entry. See complete history.

Literature

Structural insights into Deinococcus radiodurans BamA: extracellular loop diversity and its evolutionary implications

Wang, Z.Z., Xue, J.C., Wang, J.J., Yu, J.G., Qian, H.W., Yang, X.X.

(2024) JUSTC 54

DOI: https://doi.org/10.52396/JUSTC-2024-0012

Macromolecule Content

Total Structure Weight: 187.62 kDa
Atom Count: 5,580
Modeled Residue Count: 738
Deposited Residue Count: 1,756
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein assembly factor BamA	A, B	878	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 0 Gene Names: DR_0379 Membrane Entity: Yes
UniProt
Find proteins for Q9RXD5 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RXD5 Go to UniProtKB: Q9RXD5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9RXD5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	China	KY9100000034

Revision History (Full details and data files)

Version 1.0: 2025-01-15
Type: Initial release
Version 1.1: 2025-01-22
Changes: Data collection, Database references, Structure summary
Version 1.2: 2025-07-02
Changes: Data collection

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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.