1S12 | pdb_00001s12

Crystal structure of TM1457

• PDB DOI: https://doi.org/10.2210/pdb1S12/pdb

• Classification: structural genomics, unknown function
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-01-05 Released: 2004-12-07 
• Deposition Author(s): Shin, D.H., Lou, Y., Jancarik, J., Yokota, H., Kim, R., Kim, S.-H., Berkeley Structural Genomics Center (BSGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.276 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

Crystal structure of TM1457 from Thermotoga maritima.

Shin, D.H., Lou, Y., Jancarik, J., Yokota, H., Kim, R., Kim, S.H.

(2005) J Struct Biol 152: 113-117

• PubMed: 16242963 
• DOI: https://doi.org/10.1016/j.jsb.2005.08.008
• Primary Citation Related Structures: 
  1S12


• PubMed Abstract: 
  

  The crystal structure of a hypothetical protein, TM1457, from Thermotoga maritima has been determined at 2.0A resolution. TM1457 belongs to the DUF464 family (57 members) for which there is no known function. The structure shows that it is composed of two helices in contact with one side of a five-stranded beta-sheet. Two identical monomers form a pseudo-dimer in the asymmetric unit. There is a large cleft between the first alpha-helix and the second beta-strand. This cleft may be functionally important, since the two highly conserved motifs, GHA and VCAXV(S/T), are located around the cleft. A structural comparison of TM1457 with known protein structures shows the best hit with another hypothetical protein, Ybl001C from Saccharomyces cerevisiae, though they share low structural similarity. Therefore, TM1457 still retains a unique topology and reveals a novel fold.

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Organizational Affiliation: 
• College of Pharmacy, Ewha Womans University, Seoul 120-750, Korea.

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: 42.47 kDa 
• Atom Count: 3,303 
• Modeled Residue Count: 370 
• Deposited Residue Count: 376 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein TM1457	A, B, C, D	94	Thermotoga maritima	Mutation(s): 0
UniProt
Find proteins for Q9X1G8 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1G8  Go to UniProtKB:  Q9X1G8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	E [auth A], F [auth A], G [auth B], H [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.276 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.89	α = 90
b = 63.28	β = 108.01
c = 65.5	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-07 
Deposition Author(s): Shin, D.H., Lou, Y., Jancarik, J., Yokota, H., Kim, R., Kim, S.-H., Berkeley Structural Genomics Center (BSGC)

Revision History  

• Version 1.0: 2004-12-07
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-10-30
  Changes: Structure summary