9Z6R | pdb_00009z6r

Crystal Structure of CBS domain containing protein from Burkholderia phymatum

• PDB DOI: https://doi.org/10.2210/pdb9Z6R/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Paraburkholderia phymatum STM815
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-11-14 Released: 2025-11-26 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 
  0.194 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of CBS domain containing protein from Burkholderia phymatum

Ung, A.R., Lovell, S., Battaile, K.P.

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

Macromolecule Content 

• Total Structure Weight: 28.46 kDa 
• Atom Count: 2,021 
• Modeled Residue Count: 237 
• Deposited Residue Count: 256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CBS domain containing protein	A, B	128	Paraburkholderia phymatum STM815	Mutation(s): 0  Gene Names: Bphy_4760
UniProt
Find proteins for B2JRV0 (Paraburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 / STM815)) Explore B2JRV0  Go to UniProtKB:  B2JRV0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	F [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	D [auth A], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free:  0.194 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M39Z6R

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.947	α = 90
b = 40.742	β = 93.11
c = 67.579	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release