3EZY | pdb_00003ezy

Crystal structure of probable dehydrogenase TM_0414 from Thermotoga maritima

• PDB DOI: https://doi.org/10.2210/pdb3EZY/pdb

• Classification: structural genomics, unknown function
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-10-24 Released: 2009-01-13 
• Deposition Author(s): Ramagopal, U.A., Toro, R., Freeman, J., Chang, S., Maletic, M., Gheyi, T., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.223 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

Crystal structure of probable dehydrogenase TM_0414 from Thermotoga maritima

Ramagopal, U.A., Toro, R., Freeman, J., Chang, S., Maletic, M., Gheyi, T., Burley, S.K., Almo, S.C.

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: 155.62 kDa 
• Atom Count: 11,217 
• Modeled Residue Count: 1,328 
• Deposited Residue Count: 1,376 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dehydrogenase	A, B, C, D	344	Thermotoga maritima	Mutation(s): 0  Gene Names: TM_0414 EC: 1.1.1.18
UniProt
Find proteins for Q9WYP5 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYP5  Go to UniProtKB:  Q9WYP5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRD	E [auth A], F [auth B], I [auth D]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
MPD	G [auth C], H [auth C]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.223 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.144	α = 90
b = 108.739	β = 96.26
c = 98.496	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL2Map	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-13 
Deposition Author(s): Ramagopal, U.A., Toro, R., Freeman, J., Chang, S., Maletic, M., Gheyi, T., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-01-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references