9K3C | pdb_00009k3c

Crystal Structure of CapA2 from Alistipes finegoldii in complex with PLP cofactor

• PDB DOI: https://doi.org/10.2210/pdb9K3C/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Alistipes finegoldii DSM 17242
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-10-18 Released: 2025-10-22 
• Deposition Author(s): 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: 2.38 Å
• R-Value Free: 
  0.229 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: in silico

Literature

Crystal Structure of CapA2 from Alistipes finegoldii in complex with PLP cofactor

Zhang, Y., Yang, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content 

• Total Structure Weight: 48.34 kDa 
• Atom Count: 3,508 
• Modeled Residue Count: 430 
• Deposited Residue Count: 435 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteate synthase	A	435	Alistipes finegoldii DSM 17242	Mutation(s): 0  Gene Names: Alfi_3017
UniProt
Find proteins for I3YQJ3 (Alistipes finegoldii (strain DSM 17242 / JCM 16770 / CCUG 46020 / CIP 107999 / KCTC 15236 / AHN 2437)) Explore I3YQJ3  Go to UniProtKB:  I3YQJ3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP (Subject of Investigation/LOI)	C [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
CIT	B [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.229 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.821	α = 90
b = 88.511	β = 90
c = 95.117	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): 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