9BKA | pdb_00009bka

Crystal structure of Rid family protein PSPTO3006

• PDB DOI: https://doi.org/10.2210/pdb9BKA/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas syringae pv. tomato
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2024-04-26 Released: 2024-09-04 
• Deposition Author(s): Zhou, D., Chen, L., Rose, J.P., Wang, B.C.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.198 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of Rid family protein PSPTO3006

Zhou, D., Chen, L., Rose, J.P., Wang, B.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 15.13 kDa 
• Atom Count: 1,084 
• Modeled Residue Count: 132 
• Deposited Residue Count: 144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rid family protein PSPTO3006	A	144	Pseudomonas syringae pv. tomato	Mutation(s): 0  Gene Names: PSPTO_3006
UniProt
Find proteins for Q880Z0 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)) Explore Q880Z0  Go to UniProtKB:  Q880Z0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.198 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.307	α = 90
b = 71.307	β = 90
c = 71.307	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Zhou, D., Chen, L., Rose, J.P., Wang, B.C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release