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)

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
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Ligand Structure Quality Assessment

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Literature

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

Zhang, Y., Yang, S.

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I3YQJ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP (Subject of Investigation/LOI) Query on PLP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-22

Deposition Author(s):

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

Revision History (Full details and data files)

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

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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.