1T9K | pdb_00001t9k

X-ray crystal structure of aIF-2B alpha subunit-related translation initiation factor [Thermotoga maritima]

• PDB DOI: https://doi.org/10.2210/pdb1T9K/pdb

• Classification: ISOMERASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-05-17 Released: 2004-06-08 
• Deposition Author(s): Osipiuk, J., Skarina, T., Savchenko, A., Edwards, A., Cymborowski, M., Minor, W., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.298 (Depositor), 0.302 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.245 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Literature

X-ray crystal structure of aIF-2B translation initiation factor from Thermotoga maritima

Osipiuk, J., Skarina, T., Savchenko, A., Edwards, A., Cymborowski, M., Minor, W., Joachimiak, A.

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)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 155.89 kDa 
• Atom Count: 10,854 
• Modeled Residue Count: 1,364 
• Deposited Residue Count: 1,388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable methylthioribose-1-phosphate isomerase	A, B, C, D	347	Thermotoga maritima	Mutation(s): 9  Gene Names: MTNA, TM0911 EC: 5.3.1.23
UniProt
Find proteins for Q9X013 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X013  Go to UniProtKB:  Q9X013

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], H [auth B], I [auth C], J [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	F [auth A], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE	A, B, C, D	MET	Selenomethionine	C5 H11 N O2 Se

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.298 (Depositor), 0.302 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.245 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.885	α = 90
b = 103.885	β = 90
c = 259.929	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHELXD	phasing
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-06-08 
Deposition Author(s): Osipiuk, J., Skarina, T., Savchenko, A., Edwards, A., Cymborowski, M., Minor, W., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2004-06-08
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-11-06
  Changes: Data collection, Structure summary