3HIM | pdb_00003him

The Crystal Structure of a Bacterial Regulatory Protein in the tetR Family from Rhodococcus RHA1 to 2.2A

PDB DOI: https://doi.org/10.2210/pdb3HIM/pdb

Classification: TRANSCRIPTION REGULATOR
Organism(s): Rhodococcus jostii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-05-20 Released: 2009-05-26
Deposition Author(s): Stein, A.J., Binkowski, T.A., Evdokimova, E., Kagan, O., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.248 (Depositor), 0.250 (DCC)
R-Value Work:
0.197 (Depositor), 0.200 (DCC)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The Crystal Structure of a Bacterial Regulatory Protein in the tetR Family from Rhodococcus RHA1 to 2.2A

Stein, A.J., Binkowski, T.A., Evdokimova, E., Kagan, O., Edwards, A., Savchenko, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 45.36 kDa
Atom Count: 2,977
Modelled Residue Count: 382
Deposited Residue Count: 422
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable transcriptional regulator	A, B	211	Rhodococcus jostii	Mutation(s): 0
UniProt
Find proteins for Q0SD48 (Rhodococcus jostii (strain RHA1)) Explore Q0SD48 Go to UniProtKB: Q0SD48
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0SD48
Sequence Annotations Expand
Reference Sequence LOADING

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.248 (Depositor), 0.250 (DCC)
R-Value Work: 0.197 (Depositor), 0.200 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.053	α = 90
b = 63.042	β = 90
c = 94.766	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	phasing
SHELX	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-05-26

Deposition Author(s):

Binkowski, T.A.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-05-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references

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.