5DUK | pdb_00005duk

N-terminal structure of putative DNA binding transcription factor from Thermoplasmatales archaeon SCGC AB-539-N05

• PDB DOI: https://doi.org/10.2210/pdb5DUK/pdb

• Classification: TRANSCRIPTION
• Organism(s): Thermoplasmatales archaeon SCGC AB-539-N05
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-09-18 Released: 2015-10-07 
• Deposition Author(s): Chang, C., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.253 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Literature

N-terminal structure of putative DNA binding transcription factor from Thermoplasmatales archaeon SCGC AB-539-N05

Chang, C., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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: 18.48 kDa 
• Atom Count: 1,110 
• Modeled Residue Count: 127 
• Deposited Residue Count: 154 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative DNA binding protein	A, B	77	Thermoplasmatales archaeon SCGC AB-539-N05	Mutation(s): 0  Gene Names: MBGDN05_00160

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.253 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.179	α = 90
b = 43.179	β = 90
c = 194.54	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing
SBC-Collect	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-07 
Deposition Author(s): Chang, C., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2015-10-07
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary