3SHO | pdb_00003sho

Crystal structure of RpiR transcription factor from Sphaerobacter thermophilus (sugar isomerase domain)

PDB DOI: https://doi.org/10.2210/pdb3SHO/pdb

Classification: TRANSCRIPTION REGULATOR
Organism(s): Sphaerobacter thermophilus DSM 20745
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2011-06-16 Released: 2011-08-10
Deposition Author(s): Michalska, K., Tesar, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.209 (Depositor), 0.212 (DCC)
R-Value Work:
0.173 (Depositor), 0.174 (DCC)
R-Value Observed:
0.173 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of RpiR transcription factor from Sphaerobacter thermophilus (sugar isomerase domain)

Michalska, K., Tesar, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 80.48 kDa
Atom Count: 5,786
Modeled Residue Count: 731
Deposited Residue Count: 748
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, RpiR family	A, B, C, D	187	Sphaerobacter thermophilus DSM 20745	Mutation(s): 0 Gene Names: Sthe_3042
UniProt
Find proteins for D1C9F1 (Sphaerobacter thermophilus (strain ATCC 49802 / DSM 20745 / KCCM 41009 / NCIMB 13125 / S 6022)) Explore D1C9F1 Go to UniProtKB: D1C9F1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D1C9F1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 2 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
OCS Query on OCS	A, B, C, D	L-PEPTIDE LINKING	C₃ H₇ N O₅ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.209 (Depositor), 0.212 (DCC)
R-Value Work: 0.173 (Depositor), 0.174 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.194	α = 90
b = 77.816	β = 94.89
c = 71.157	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELX	model building
MLPHARE	phasing
DM	model building
ARP/wARP	model building
Coot	model building
BUSTER	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
DM	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-08-10

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2011-08-10
Type: Initial release
Version 1.1: 2025-03-26
Changes: Data collection, Database references, Derived calculations, Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.