Macromolecule Content

Total Structure Weight: 25.86 kDa
Atom Count: 1,847
Modelled Residue Count: 210
Deposited Residue Count: 212
Unique protein chains: 1

3RH2

Crystal structure of a TetR-like transcriptional regulator (Sama_0099) from Shewanella amazonensis SB2B at 2.42 A resolution

PDB DOI: 10.2210/pdb3RH2/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Shewanella amazonensis SB2B
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-04-11 Released: 2011-05-04
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.250
R-Value Work: 0.205
R-Value Observed: 0.207

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a Hypothetical TetR-like transcriptional regulator (Sama_0099) from SHEWANELLA AMAZONENSIS SB2B at 2.42 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical TetR-like transcriptional regulator	A	212	Shewanella amazonensis SB2B	Mutation(s): 0 Gene Names: Sama_0099
UniProt
Find proteins for A1S1Q5 (Shewanella amazonensis (strain ATCC BAA-1098 / SB2B)) Explore A1S1Q5 Go to UniProtKB: A1S1Q5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1S1Q5
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Ligand Interaction
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A]	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
UNL Query on UNL Download Ideal Coordinates CCD File	B [auth A]	Unknown ligand PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.250
R-Value Work: 0.205
R-Value Observed: 0.207
Space Group: P 4₃ 2₁ 2
Diffraction Data DOI: 10.18430/M33RH2 Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.536	α = 90
b = 123.536	β = 90
c = 49.552	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction
SHELXD	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-05-04

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2011-05-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2014-12-24
Changes: Structure summary
Version 1.3: 2017-11-08
Changes: Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.