3IHU

Crystal structure of DNA binding protein (YP_298823.1) from Ralstonia eutropha JMP134 at 1.92 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3IHU/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Cupriavidus pinatubonensis JMP134
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-30 Released: 2009-08-11 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.237 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Literature

Crystal structure of DNA binding protein (YP_298823.1) from Ralstonia eutropha JMP134 at 1.92 A resolution

Joint Center for Structural Genomics (JCSG)

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 49.03 kDa 
• Atom Count: 3,411 
• Modelled Residue Count: 409 
• Deposited Residue Count: 444 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, GntR family	A, B	222	Cupriavidus pinatubonensis JMP134	Mutation(s): 0  Gene Names: Reut_B4629, YP_298823.1
UniProt
Find proteins for Q46SA5 (Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197)) Explore Q46SA5  Go to UniProtKB:  Q46SA5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth B], D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 1.92 Å
• R-Value Free: 0.237 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.18430/M33IHU

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.646	α = 90
b = 79.135	β = 102.08
c = 103.244	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-11 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-08-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations