9W96 | pdb_00009w96

Crystal structure of BioZ C115S from Agrobacterium tumefaciens in complex with galutaryl-CoA

• PDB DOI: https://doi.org/10.2210/pdb9W96/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-08-09 Released: 2025-10-29 
• Deposition Author(s): Zhang, L., Zhang, L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.254 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of BioZ C115S from Agrobacterium tumefaciens in complex with galutaryl-CoA

Zhang, L., Zhang, L.

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: gel filtration

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: 139.62 kDa 
• Atom Count: 9,931 
• Modeled Residue Count: 1,307 
• Deposited Residue Count: 1,308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxopimeloyl-[acyl-carrier-protein] synthase	A, B, C, D	327	Agrobacterium fabrum str. C58	Mutation(s): 1  Gene Names: bioZ, fabH2, Atu4001 EC: 2.3.1
UniProt
Find proteins for Q7CTU0 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7CTU0  Go to UniProtKB:  Q7CTU0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GRA (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	glutaryl-coenzyme A C26 H42 N7 O19 P3 S SYKWLIJQEHRDNH-CKRMAKSASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.254 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.718	α = 90
b = 128.453	β = 90
c = 170.961	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Zhang, L., Zhang, L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22477077

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release