3SXK | pdb_00003sxk

Zn2+-bound FCD domain of TM0439, a putative transcriptional regulator

• PDB DOI: https://doi.org/10.2210/pdb3SXK/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 
  0.192 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Zn2+-bound FCD domain of TM0439, a putative transcriptional regulator

Czelakowski, G.P., Derewenda, Z.S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.5 kDa 
• Atom Count: 2,653 
• Modeled Residue Count: 278 
• Deposited Residue Count: 280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, GntR family	A, B	140	Thermotoga maritima	Mutation(s): 3  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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	D [auth A], E [auth A], H [auth B], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
BCT	F [auth A], J [auth B]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free:  0.192 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.697	α = 90
b = 79.977	β = 115.08
c = 49.223	γ = 90

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

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  

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