9K2P | pdb_00009k2p

The crystal structure of CapA1 from Capnocytophaga ochracea

• PDB DOI: https://doi.org/10.2210/pdb9K2P/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Capnocytophaga ochracea DSM 7271
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-10-17 Released: 2025-10-22 
• Deposition Author(s): Zhang, L., Yang, S., Zhang, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 
  0.208 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: in silico

Literature

The crystal structure of CapA1 from Capnocytophaga ochracea

Yang, S., Zhang, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: assay for oligomerization

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 74.16 kDa 
• Atom Count: 5,842 
• Modeled Residue Count: 666 
• Deposited Residue Count: 666 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxal-5'-phosphate-dependent protein beta subunit	A, B	333	Capnocytophaga ochracea DSM 7271	Mutation(s): 0  Gene Names: Coch_1829 EC: 2.5.1.76
UniProt
Find proteins for C7M8J5 (Capnocytophaga ochracea (strain ATCC 27872 / DSM 7271 / CCUG 9716 / JCM 12966 / NCTC 12371 / SS31 / VPI 2845)) Explore C7M8J5  Go to UniProtKB:  C7M8J5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free:  0.208 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.83	α = 90
b = 107.11	β = 90
c = 122.04	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Zhang, L., Yang, S., Zhang, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release