4G97 | pdb_00004g97

Crystal structure of the response regulator PhyR from Brucella abortus

• PDB DOI: https://doi.org/10.2210/pdb4G97/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Brucella abortus 2308
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-07-23 Released: 2014-03-12 
• Deposition Author(s): Klinke, S., Sycz, G., Rinaldi, J.J., Paris, G., Goldbaum, F.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.247 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the response regulator PhyR from Brucella abortus

Klinke, S., Sycz, G., Rinaldi, J.J., Paris, G., Goldbaum, F.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 29.94 kDa 
• Atom Count: 1,870 
• Modeled Residue Count: 243 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Response regulator receiver	A	270	Brucella abortus 2308	Mutation(s): 0  Gene Names: BAB1_1671, PhyR
UniProt
Find proteins for Q2YRH9 (Brucella abortus (strain 2308)) Explore Q2YRH9  Go to UniProtKB:  Q2YRH9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.247 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.37	α = 90
b = 53.37	β = 90
c = 177.3	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
AMoRE	phasing
BUSTER	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-12 
Deposition Author(s): Klinke, S., Sycz, G., Rinaldi, J.J., Paris, G., Goldbaum, F.A.

Revision History  

• Version 1.0: 2014-03-12
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description