9BKB | pdb_00009bkb

Crystal structure of Rid family protein ACIAD3089 from Acinetobacter baylyi

• PDB DOI: https://doi.org/10.2210/pdb9BKB/pdb

• Classification: HYDROLASE
• Organism(s): Acinetobacter baylyi
• 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: 2.10 Å
• R-Value Free: 
  0.222 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of Rid family protein ACIAD3089 from Acinetobacter baylyi

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.

Macromolecule Content 

• Total Structure Weight: 53.37 kDa 
• Atom Count: 3,578 
• Modeled Residue Count: 453 
• Deposited Residue Count: 489 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rid family protein ACIAD3089	A, B, C	163	Acinetobacter baylyi	Mutation(s): 0  Gene Names: ACIAD3089
UniProt
Find proteins for Q6F828 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)) Explore Q6F828  Go to UniProtKB:  Q6F828

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.222 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.41	α = 90
b = 87.41	β = 90
c = 183.68	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