3C7J | pdb_00003c7j

Crystal structure of transcriptional regulator (GntR family member) from Pseudomonas syringae pv. tomato str. DC3000

• PDB DOI: https://doi.org/10.2210/pdb3C7J/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Pseudomonas syringae pv. tomato str. DC3000
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-02-07 Released: 2008-02-26 
• Deposition Author(s): Nocek, B., Sather, A., Gu, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.227 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Structure of transcriptional regulator (GntR family member) from Pseudomonas syringae pv. tomato str. DC3000.

Nocek, B., Sather, A., Gu, M., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 53.7 kDa 
• Atom Count: 4,037 
• Modeled Residue Count: 464 
• Deposited Residue Count: 474 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, GntR family	A, B	237	Pseudomonas syringae pv. tomato str. DC3000	Mutation(s): 0  Gene Names: PSPTO5454
UniProt
Find proteins for Q19AK4 (Pseudomonas syringae pv. syringae) Explore Q19AK4  Go to UniProtKB:  Q19AK4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	C [auth A], D [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-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: 2.10 Å
• R-Value Free:  0.227 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.954	α = 90
b = 132.768	β = 90
c = 170.461	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
Coot	model building
MLPHARE	phasing
PHENIX	phasing
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-26 
Deposition Author(s): Nocek, B., Sather, A., Gu, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-02-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary