9Q6A | pdb_00009q6a

Crystal structure of octameric COMMD-like protein MBK5214510 from Flavobacteriaceae bacterium

PDB DOI: https://doi.org/10.2210/pdb9Q6A/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Flavobacteriaceae bacterium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-08-21 Released: 2025-10-01
Deposition Author(s): Collins, B.M., Healy, M.D., Liu, M.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.58 Å
R-Value Free:
0.292 (Depositor), 0.292 (DCC)
R-Value Work:
0.239 (Depositor), 0.240 (DCC)
R-Value Observed:
0.245 (Depositor)

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

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

Literature

The prokaryotic origins of the COMMD protein family involved in eukaryotic membrane trafficking

Collins, B.M., Healy, M.D., Liu, M.

To be published.

Macromolecule Content

Total Structure Weight: 55.5 kDa
Atom Count: 3,492
Modeled Residue Count: 427
Deposited Residue Count: 480
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COMMD-like protein MBK5214510	A, B	240	Flavobacteriaceae bacterium	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.58 Å
R-Value Free: 0.292 (Depositor), 0.292 (DCC)
R-Value Work: 0.239 (Depositor), 0.240 (DCC)
R-Value Observed: 0.245 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.343	α = 90
b = 96.013	β = 90
c = 115.614	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-01

Deposition Author(s):

Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	--

Revision History (Full details and data files)

Version 1.0: 2025-10-01
Type: Initial release

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.