4J1T | pdb_00004j1t

Crystal structure of Thermus thermophilus transhydrogenase heterotrimeric complex of the Alpha1 subunit dimer with the NADP binding domain (domain III) of the Beta subunit in P2(1)

• PDB DOI: https://doi.org/10.2210/pdb4J1T/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermus thermophilus HB27
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-02-02 Released: 2014-02-05 
• Deposition Author(s): Yamaguchi, M., Leung, J., Schurig Briccio, L.A., Gennis, R.B., Stout, C.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Crystal structure analysis of Thermus thermophilus transhydrogenase soluble domains

Yamaguchi, M., Leung, J., Schurig Briccio, L.A., Gennis, R.B., Stout, C.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

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

Macromolecule Content

• Total Structure Weight: 206.62 kDa 
• Atom Count: 14,253 
• Modelled Residue Count: 1,835 
• Deposited Residue Count: 1,894 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD/NADP transhydrogenase alpha subunit 1	A, B, D, E	381	Thermus thermophilus HB27	Mutation(s): 0  Gene Names: TT_C1780 EC: 1.6.1.2 (PDB Primary Data), 7.1.1.1 (UniProt)
UniProt
Find proteins for Q72GR8 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72GR8  Go to UniProtKB:  Q72GR8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P) transhydrogenase subunit beta	C, F	185	Thermus thermophilus HB27	Mutation(s): 0  EC: 1.6.1.2 (PDB Primary Data), 7.1.1.1 (UniProt)
UniProt
Find proteins for Q72GS0 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72GS0  Go to UniProtKB:  Q72GS0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	I [auth C], N [auth F]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
NAD	H [auth B], M [auth E]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
GOL	G [auth A], J [auth D], K [auth D], L [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.075	α = 90
b = 68.866	β = 91.03
c = 132.335	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-05 
Deposition Author(s): Yamaguchi, M., Leung, J., Schurig Briccio, L.A., Gennis, R.B., Stout, C.D.

Revision History  

• Version 1.0: 2014-02-05
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description