1MP9 | pdb_00001mp9

TBP from a mesothermophilic archaeon, Sulfolobus acidocaldarius

• PDB DOI: https://doi.org/10.2210/pdb1MP9/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Sulfolobus acidocaldarius
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-09-12 Released: 2003-11-04 
• Deposition Author(s): Koike, H., Kawashima-Ohya, Y., Yamasaki, T., Clowney, L., Katsuya, Y., Suzuki, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.254 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Origins of Protein Stability Revealed by Comparing Crystal Structures of TATA Binding Proteins.

Koike, H., Kawashima-Ohya, Y., Yamasaki, T., Clowney, L., Katsuya, Y., Suzuki, M.

(2004) Structure 12: 157-168

• PubMed: 14725775 
• DOI: https://doi.org/10.1016/j.str.2003.12.003
• Primary Citation Related Structures: 
  1MP9


• PubMed Abstract: 
  

  The crystal structure of TATA binding protein (TBP) from a mesothermophilic archaeon, Sulfolobus acidocaldarius, has been determined at a resolution of 2.0 A with an R factor of 20.9%. By comparing this structure with the structures of TBPs from a hyperthermophilic archaeon and mesophilic eukaryotes, as well as by comparing amino acid sequences of TBPs from archaea, covering a wide range of optimum growth temperatures, two significant determinants of the stability of TBP have been identified: increasing the interior hydrophobicity by interaction between three residues, Val, Leu, and Ile, with further differentiation of the surface, and increasing its hydrophilicity and raising the cost of unfolding. These findings suggest directions along which the stability of TBP can be engineered.

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Organizational Affiliation: 
• National Institute of Advanced Industrial Science and Technology, AIST Tsukuba Center 6-10, Higashi 1-1-1, Tsukuba 305-8566, Japan.

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: 45 kDa 
• Atom Count: 3,333 
• Modeled Residue Count: 382 
• Deposited Residue Count: 396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TATA-binding protein	A, B	198	Sulfolobus acidocaldarius	Mutation(s): 0
UniProt
Find proteins for Q9UWN7 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)) Explore Q9UWN7  Go to UniProtKB:  Q9UWN7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.254 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.9	α = 90
b = 80.4	β = 90
c = 86.6	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-11-04 
Deposition Author(s): Koike, H., Kawashima-Ohya, Y., Yamasaki, T., Clowney, L., Katsuya, Y., Suzuki, M.

Revision History  

• Version 1.0: 2003-11-04
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references