9J6E | pdb_00009j6e

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

• PDB DOI: https://doi.org/10.2210/pdb9J6E/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-15 Released: 2025-08-20 
• 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: 2.15 Å
• R-Value Free: 
  0.231 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of BioZ 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: 140.21 kDa 
• Atom Count: 10,114 
• Modeled Residue Count: 1,308 
• Deposited Residue Count: 1,312 
• 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	328	Agrobacterium fabrum str. C58	Mutation(s): 0  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
COA	E [auth A], F [auth B], G [auth C], H [auth D]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A1ECI	A, B, C, D	L-PEPTIDE LINKING	C8 H13 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.231 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.681	α = 90
b = 126.691	β = 102.91
c = 84.856	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): Zhang, L., Zhang, L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22077081

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release