2RGY

Crystal structure of transcriptional regulator of LacI family from Burkhoderia phymatum

• PDB DOI: https://doi.org/10.2210/pdb2RGY/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Paraburkholderia phymatum STM815
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-10-05 Released: 2007-10-23 
• Deposition Author(s): Agarwal, R., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.267 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 

Literature

Structural analysis of transcription regulator of LacI family from Burkholderia phymatum.

Agarwal, R., Burley, S.K., Swaminathan, S.

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)

Macromolecule Content

• Total Structure Weight: 32.17 kDa 
• Atom Count: 2,296 
• Modelled Residue Count: 275 
• Deposited Residue Count: 290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, LacI family	A	290	Paraburkholderia phymatum STM815	Mutation(s): 0  Gene Names: BphyDRAFT_4885
UniProt
Find proteins for B2JNW3 (Paraburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 / STM815)) Explore B2JNW3  Go to UniProtKB:  B2JNW3

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.267 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.543	α = 90
b = 118.777	β = 90
c = 85.439	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
SHELXE	model building
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-23 
Deposition Author(s): Agarwal, R., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-10-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary