1O2D

Crystal structure of Alcohol dehydrogenase, iron-containing (TM0920) from Thermotoga maritima at 1.30 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1O2D/pdb
• Entry: 1O2D supersedes: 1J5R

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


• Deposited: 2003-02-27 Released: 2003-06-10 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.170 
• R-Value Work: 0.137 
• R-Value Observed: 0.139 

Literature

Crystal structure of an iron-containing 1,3-propanediol dehydrogenase (TM0920) from Thermotoga maritima at 1.3 A resolution

Schwarzenbacher, R., von Delft, F., Canaves, J.M., Brinen, L.S., Dai, X., Deacon, A.M., Elsliger, M.A., Eshaghi, S., Floyd, R., Godzik, A., Grittini, C., Grzechnik, S.K., Guda, C., Jaroszewski, L., Karlak, C., Klock, H.E., Koesema, E., Kovarik, J.S., Kreusch, A., Kuhn, P., Lesley, S.A., McMullan, D., McPhillips, T.M., Miller, M.A., Miller, M.D., Morse, A., Moy, K., Ouyang, J., Page, R., Robb, A., Rodrigues, K., Selby, T.L., Spraggon, G., Stevens, R.C., van den Bedem, H., Velasquez, J., Vincent, J., Wang, X., West, B., Wolf, G., Hodgson, K.O., Wooley, J., Wilson, I.A.

(2004) Proteins 54: 174-177

• PubMed: 14705036 
• DOI: https://doi.org/10.1002/prot.10594
• Primary Citation of Related Structures:  
  1O2D

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Organizational Affiliation: 

The Joint Center for Structural Genomics, California 92037, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 85.73 kDa 
• Atom Count: 6,604 
• Modelled Residue Count: 719 
• Deposited Residue Count: 742 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alcohol dehydrogenase, iron-containing	A, B	371	Thermotoga maritima	Mutation(s): 11  Gene Names: TM0920 EC: 1.1.1.1
UniProt
Find proteins for Q9X022 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X022  Go to UniProtKB:  Q9X022

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	D [auth A], G [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
TRS	E [auth A], H [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
FE	C [auth A], F [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.170 
• R-Value Work: 0.137 
• R-Value Observed: 0.139 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M31O2D

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.047	α = 90
b = 85.283	β = 96.29
c = 72.08	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
RESOLVE	model building
SOLVE	phasing
REFMAC	refinement
CCP4	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-06-10 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)
• This entry supersedes: 1J5R

Revision History  

• Version 1.0: 2003-06-10
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2018-07-18
  Changes: Data collection, Database references
• Version 1.5: 2023-01-25
  Changes: Database references, Derived calculations