3IP3

Structure of putative oxidoreductase (TM_0425) from Thermotoga maritima

PDB DOI: https://doi.org/10.2210/pdb3IP3/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermotoga maritima
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-08-16 Released: 2009-09-29
Deposition Author(s): Ramagopal, U.A., Morano, C., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.242
R-Value Work: 0.204
R-Value Observed: 0.206

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure of putative oxidoreductase (TM_0425) from Thermotoga maritima

Ramagopal, U.A., Morano, C., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 311.21 kDa
Atom Count: 21,415
Modelled Residue Count: 2,631
Deposited Residue Count: 2,696
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase, putative	A, B, C, D, E A, B, C, D, E, F, G, H	337	Thermotoga maritima	Mutation(s): 0 Gene Names: TM_0425
UniProt
Find proteins for Q9WYQ6 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYQ6 Go to UniProtKB: Q9WYQ6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9WYQ6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth F] SDF format, chain M [auth F] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth F] MOL2 format, chain M [auth F]	I [auth A], J [auth B], K [auth B], L [auth F], M [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth F] Focus chain M [auth F] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth F] Focus chain M [auth F]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.242
R-Value Work: 0.204
R-Value Observed: 0.206
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.009	α = 90
b = 94.181	β = 91.91
c = 142.852	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
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-09-29

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-09-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2021-02-10
Changes: Database references, Derived calculations, Structure summary

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3IP3

Structure of putative oxidoreductase (TM_0425) from Thermotoga maritima

Structure of putative oxidoreductase (TM_0425) from Thermotoga maritima

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)