3R4K

Crystal structure of a putative ICLR transcriptional regulator (TM1040_3717) from SILICIBACTER SP. TM1040 at 2.46 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3R4K/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Ruegeria sp. TM1040
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-03-17 Released: 2011-04-13 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 0.231 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Literature

Crystal structure of a putative ICLR transcriptional regulator (TM1040_3717) from SILICIBACTER SP. TM1040 at 2.46 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 111.91 kDa 
• Atom Count: 7,933 
• Modelled Residue Count: 1,017 
• Deposited Residue Count: 1,040 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, IclR family	A, B, C, D	260	Ruegeria sp. TM1040	Mutation(s): 0  Gene Names: TM1040_3717
UniProt
Find proteins for Q1GKY2 (Ruegeria sp. (strain TM1040)) Explore Q1GKY2  Go to UniProtKB:  Q1GKY2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth B], F [auth B], G [auth C], H [auth C], I [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 0.231 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: P 2₁ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M33R4K

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 203.983	α = 90
b = 75.523	β = 90
c = 77.01	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
BUSTER-TNT	refinement
MOSFLM	data reduction
SHELXD	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-13 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2011-04-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-02-01
  Changes: Database references, Derived calculations