3GRA | pdb_00003gra

Crystal structure of AraC family transcriptional regulator from Pseudomonas putida

• PDB DOI: https://doi.org/10.2210/pdb3GRA/pdb

• Classification: Transcription regulator
• Organism(s): Pseudomonas putida KT2440
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-25 Released: 2009-04-14 
• Deposition Author(s): Bagaria, A., Kumaran, D., 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: 2.30 Å
• R-Value Free: 
  0.288 (Depositor), 0.291 (DCC) 
• R-Value Work: 
  0.268 (Depositor), 0.283 (DCC) 
• R-Value Observed: 
  0.268 (Depositor) 

Literature

Crystal structure of AraC family transcriptional regulator from Pseudomonas putida

Bagaria, A., Kumaran, D., 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: 44.85 kDa 
• Atom Count: 2,670 
• Modeled Residue Count: 345 
• Deposited Residue Count: 404 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, AraC family	A, B	202	Pseudomonas putida KT2440	Mutation(s): 0  Gene Names: PP_3526, PP3526
UniProt
Find proteins for Q88H39 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88H39  Go to UniProtKB:  Q88H39

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.288 (Depositor), 0.291 (DCC) 
• R-Value Work:  0.268 (Depositor), 0.283 (DCC) 
• R-Value Observed: 0.268 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.852	α = 90
b = 71.876	β = 90
c = 104.518	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHARP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-14 
Deposition Author(s): Bagaria, A., Kumaran, D., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Structure summary