2YW9 | pdb_00002yw9

Crystal structure of TT0143 from Thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb2YW9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-04-20 Released: 2007-05-15 
• Deposition Author(s): Miyano, M., Ago, H., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.263 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of TT0143 from Thermus thermophilus HB8

Ago, H., Hamada, K., Ida, K., Kanda, H., Sugahara, M., Yamamoto, M., Nodake, Y., Kuramitsu, S., Yokoyama, S., Miyano, M.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 226.62 kDa 
• Atom Count: 14,777 
• Modeled Residue Count: 1,978 
• Deposited Residue Count: 2,088 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-[acyl carrier protein] reductase	A, B, C, D, E, F, G, H	261	Thermus thermophilus HB8	Mutation(s): 0  EC: 1.3.1.10 (PDB Primary Data), 1.3.1.9 (UniProt)
UniProt
Find proteins for Q5SLI9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLI9  Go to UniProtKB:  Q5SLI9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	I [auth D], J [auth H]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.263 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.087	α = 90
b = 107.131	β = 90
c = 184.704	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-15 
Deposition Author(s): Miyano, M., Ago, H., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-05-15
  Type: Initial release
  
• Version 1.1: 2007-10-04
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description