9HMU | pdb_00009hmu

DUF4465 domain containing protein in complex with vitamin B12.

• PDB DOI: https://doi.org/10.2210/pdb9HMU/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Coraliomargarita akajimensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-12-09 Released: 2025-01-15 
• Deposition Author(s): Clarke, C., Banasik, M., Pickersgill, R.W.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.213 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 

Starting Model: in silico

Literature

DUF4465 domains bind vitamin B12.

Clarke, C., Banasik, M., Pickersgill, R.W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 85.03 kDa 
• Atom Count: 6,073 
• Modeled Residue Count: 670 
• Deposited Residue Count: 750 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF4465 domain containing protein D5EK	A, B, C	250	Coraliomargarita akajimensis	Mutation(s): 0  Gene Names: Caka_1781
UniProt
Find proteins for D5EK51 (Coraliomargarita akajimensis (strain DSM 45221 / IAM 15411 / JCM 23193 / KCTC 12865 / 04OKA010-24)) Explore D5EK51  Go to UniProtKB:  D5EK51

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CNC (Subject of Investigation/LOI)	D [auth A], F [auth B], H [auth C]	CYANOCOBALAMIN C63 H89 Co N14 O14 P SYZBZQWSWIJYAR-UVKKECPRSA-M
CA (Subject of Investigation/LOI)	E [auth A], G [auth B], I [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.213 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.72	α = 90
b = 113.72	β = 90
c = 162.593	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-15 
Deposition Author(s): Clarke, C., Banasik, M., Pickersgill, R.W.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	--

Revision History  

• Version 1.0: 2025-01-15
  Type: Initial release
  
• Version 1.1: 2025-01-22
  Changes: Structure summary