2ZBC | pdb_00002zbc

Crystal structure of STS042, a stand-alone RAM module protein, from hyperthermophilic archaeon Sulfolobus tokodaii strain7.

• PDB DOI: https://doi.org/10.2210/pdb2ZBC/pdb

• Classification: TRANSCRIPTION
• Organism(s): Sulfurisphaera tokodaii str. 7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-10-19 Released: 2008-03-11 
• Deposition Author(s): Miyazono, K., Tsujimura, M., Kawarabayasi, Y., Tanokura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.219 (Depositor) 
• R-Value Work: 
  0.170 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Literature

Crystal structure of STS042, a stand-alone RAM module protein, from hyperthermophilic archaeon Sulfolobus tokodaii strain7

Miyazono, K., Tsujimura, M., Kawarabayasi, Y., Tanokura, M.

(2008) Proteins 71: 1557-1562

• PubMed: 18300246 
• DOI: https://doi.org/10.1002/prot.21987
• Primary Citation of Related Structures:  
  2ZBC

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Organizational Affiliation: 

Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 76.49 kDa 
• Atom Count: 5,494 
• Modelled Residue Count: 648 
• Deposited Residue Count: 664 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
83aa long hypothetical transcriptional regulator asnC	A, B, C, D, E, F, G, H	83	Sulfurisphaera tokodaii str. 7	Mutation(s): 0
UniProt
Find proteins for Q975W5 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q975W5  Go to UniProtKB:  Q975W5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ILE	I [auth A], J [auth A], K [auth B], L [auth B], M [auth E], N [auth F], O [auth F], P [auth G]	ISOLEUCINE C6 H13 N O2 AGPKZVBTJJNPAG-WHFBIAKZSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.219 (Depositor) 
• R-Value Work:  0.170 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.367	α = 90
b = 61.785	β = 94.47
c = 90.487	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-11 
Deposition Author(s): Miyazono, K., Tsujimura, M., Kawarabayasi, Y., Tanokura, M.

Revision History  

• Version 1.0: 2008-03-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-11
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary