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)

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

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1GKY2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth C] SDF format, chain I [auth C] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth C] mmCIF format, chain I [auth C]	E [auth B], F [auth B], G [auth C], H [auth C], I [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth C] Focus chain I [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-04-13

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.