2VKJ | pdb_00002vkj

Structure of the soluble domain of the membrane protein TM1634 from Thermotoga maritima

• PDB DOI: https://doi.org/10.2210/pdb2VKJ/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-12-19 Released: 2008-04-08 
• Deposition Author(s): McCleverty, C.J., Columbus, L., Kreusch, A., Lesley, S.A., Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.229 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Structure and Ligand Binding of the Soluble Domain of a Thermotoga Maritima Membrane Protein of Unknown Function Tm1634.

Mccleverty, C.J., Columbus, L., Kreusch, A., Lesley, S.A.

(2008) Protein Sci 17: 869

• PubMed: 18369189 
• DOI: https://doi.org/10.1110/ps.083432208
• Primary Citation Related Structures: 
  2VKJ, 2VKO


• PubMed Abstract: 
  

  As a part of the Joint Center for Structural Genomics (JCSG) biological targets, the structures of soluble domains of membrane proteins from Thermotoga maritima were pursued. Here, we report the crystal structure of the soluble domain of TM1634, a putative membrane protein of 128 residues (15.1 kDa) and unknown function. The soluble domain of TM1634 is an alpha-helical dimer that contains a single tetratrico peptide repeat (TPR) motif in each monomer where each motif is similar to that found in Tom20. The overall fold, however, is unique and a DALI search does not identify similar folds beyond the 38-residue TPR motif. Two different putative ligand binding sites, in which PEG200 and Co(2+) were located, were identified using crystallography and NMR, respectively.

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Organizational Affiliation: 
• The Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 24.89 kDa 
• Atom Count: 1,956 
• Modeled Residue Count: 212 
• Deposited Residue Count: 212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TM1634	A, B	106	Thermotoga maritima	Mutation(s): 0
UniProt
Find proteins for Q9X1W9 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1W9  Go to UniProtKB:  Q9X1W9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.229 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.229	α = 90
b = 76.199	β = 90
c = 46.23	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-08 
Deposition Author(s): McCleverty, C.J., Columbus, L., Kreusch, A., Lesley, S.A., Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-04-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Other