2DT8 | pdb_00002dt8

Fatty Acid Binding of a DegV family Protein from Thermus thermophilus

• PDB DOI: https://doi.org/10.2210/pdb2DT8/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-07-11 Released: 2007-06-19 
• Deposition Author(s): Rehse, P.H., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.197 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Literature

Fatty Acid Binding of a DegV family Protein from Thermus thermophilus

Rehse, P.H., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 31.31 kDa 
• Atom Count: 2,525 
• Modeled Residue Count: 280 
• Deposited Residue Count: 280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DegV family protein	A	280	Thermus thermophilus HB8	Mutation(s): 3
UniProt
Find proteins for Q5SJQ7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJQ7  Go to UniProtKB:  Q5SJQ7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLM	C [auth A]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.197 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.548	α = 90
b = 36.969	β = 127.065
c = 81.461	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data processing
CNS	refinement
PDB_EXTRACT	data extraction
d*TREK	data reduction
d*TREK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-19 
Deposition Author(s): Rehse, P.H., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-06-19
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary