1VL6 | pdb_00001vl6

Crystal structure of NAD-dependent malic enzyme (TM0542) from Thermotoga maritima at 2.61 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1VL6/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-07-13 Released: 2004-08-17 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 
  0.239 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Crystal structure of NAD-dependent malic enzyme (TM0542) from Thermotoga maritima at 2.61 A resolution

Joint Center for Structural Genomics (JCSG)

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 (software)

Macromolecule Content 

• Total Structure Weight: 171.34 kDa 
• Atom Count: 11,180 
• Modeled Residue Count: 1,486 
• Deposited Residue Count: 1,552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
malate oxidoreductase	A, B, C, D	388	Thermotoga maritima MSB8	Mutation(s): 6  Gene Names: TM0542
UniProt
Find proteins for Q9WZ12 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZ12  Go to UniProtKB:  Q9WZ12

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free:  0.239 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VL6

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.963	α = 90
b = 143.963	β = 90
c = 163.428	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
MOSFLM	data reduction
SCALEPACK	data scaling
SOLVE	phasing
SHARP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-17 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-08-17
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-09
  Changes: Data collection, Refinement description, Structure summary