3HDC | pdb_00003hdc

The crystal structure of thioredoxin protein from Geobacter metallireducens

PDB DOI: https://doi.org/10.2210/pdb3HDC/pdb

Classification: OXIDOREDUCTASE
Organism(s): Geobacter metallireducens GS-15
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-05-07 Released: 2009-05-26
Deposition Author(s): Zhang, Z., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.197 (Depositor), 0.191 (DCC)
R-Value Work:
0.179 (Depositor), 0.177 (DCC)
R-Value Observed:
0.180 (Depositor)

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This is version 1.4 of the entry. See complete history.

Literature

The crystal structure of thioredoxin protein from Geobacter metallireducens

Zhang, Z., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 18 kDa
Atom Count: 1,354
Modeled Residue Count: 150
Deposited Residue Count: 158
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin family protein	A	158	Geobacter metallireducens GS-15	Mutation(s): 0 Gene Names: Gmet_1383
UniProt
Find proteins for Q39VV7 (Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15)) Explore Q39VV7 Go to UniProtKB: Q39VV7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q39VV7
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.197 (Depositor), 0.191 (DCC)
R-Value Work: 0.179 (Depositor), 0.177 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.678	α = 90
b = 63.678	β = 90
c = 94.587	γ = 120

Software Package:

Software Name	Purpose
CBASS	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-05-26

Deposition Author(s):

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-05-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2019-11-13
Changes: Derived calculations, Structure summary
Version 1.3: 2021-02-10
Changes: Database references, Structure summary
Version 1.4: 2024-10-30
Changes: Data collection, Database references, 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.