3HDC

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.197 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 

Literature

The crystal structure of thioredoxin protein from Geobacter metallireducens

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

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

Macromolecules

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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 
• 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

Entry History 

Deposition Data

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

Revision History  

• 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