1VBI | pdb_00001vbi

Crystal structure of type 2 malate/lactate dehydrogenase from thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb1VBI/pdb

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


• Deposited: 2004-02-27 Released: 2005-04-19 
• Deposition Author(s): Mizutani, H., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.210 (Depositor), 0.181 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

Crystal structure of type 2 malate/lactate dehydrogenase from thermus thermophilus HB8

Mizutani, H., Kunishima, N.

To be published.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 38.2 kDa 
• Atom Count: 2,997 
• Modeled Residue Count: 340 
• Deposited Residue Count: 344 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type 2 malate/lactate dehydrogenase	A	344	Thermus thermophilus	Mutation(s): 0  EC: 1.1.1.27
UniProt
Find proteins for Q53W84 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q53W84  Go to UniProtKB:  Q53W84

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.210 (Depositor), 0.181 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.32	α = 90
b = 78.32	β = 90
c = 253.213	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-19 
Deposition Author(s): Mizutani, H., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-04-19
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations