3SXZ | pdb_00003sxz

Metal-free FCD domain of TM0439 a putative transcriptional regulator

PDB DOI: https://doi.org/10.2210/pdb3SXZ/pdb

Classification: TRANSCRIPTION REGULATOR
Organism(s): Thermotoga maritima
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-07-15 Released: 2011-11-16
Deposition Author(s): Czelakowski, G.P., Derewenda, Z.S., Integrated Center for Structure and Function Innovation (ISFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free:
0.228 (Depositor), 0.227 (DCC)
R-Value Work:
0.197 (Depositor), 0.196 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Metal-free FCD domain of TM0439 a putative transcriptional regulator

Czelakowski, G.P., Derewenda, Z.S.

To be published.

Macromolecule Content

Total Structure Weight: 33.27 kDa
Atom Count: 2,407
Modeled Residue Count: 279
Deposited Residue Count: 280
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, GntR family	A, B	140	Thermotoga maritima	Mutation(s): 0 Gene Names: TM_0439
UniProt
Find proteins for Q9WYS0 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYS0 Go to UniProtKB: Q9WYS0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WYS0
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.228 (Depositor), 0.227 (DCC)
R-Value Work: 0.197 (Depositor), 0.196 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.89	α = 90
b = 80.89	β = 90
c = 91.739	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-11-16

Deposition Author(s):

Czelakowski, G.P.

Derewenda, Z.S.

Integrated Center for Structure and Function Innovation (ISFI)

Revision History (Full details and data files)

Version 1.0: 2011-11-16
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Refinement description

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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.