1O2D | pdb_00001o2d

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.170 (Depositor), 0.226 (DCC)
R-Value Work:
0.137 (Depositor), 0.204 (DCC)
R-Value Observed:
0.139 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1O2D

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1002/prot.10594
Primary Citation Related Structures:
1O2D

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X022
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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 (Depositor), 0.226 (DCC)
R-Value Work: 0.137 (Depositor), 0.204 (DCC)
R-Value Observed: 0.139 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2003-06-10

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

This entry supersedes: 1J5R

Revision History (Full details and data files)

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
Version 1.6: 2024-11-20
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.