3GL3 | pdb_00003gl3

Crystal structure of a putative Thiol:disulfide interchange protein DsbE from Chlorobium tepidum

• PDB DOI: https://doi.org/10.2210/pdb3GL3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Chlorobaculum tepidum TLS
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-11 Released: 2009-03-31 
• Deposition Author(s): Damodharan, L., 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: 2.09 Å
• R-Value Free: 
  0.296 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.263 (Depositor), 0.280 (DCC) 
• R-Value Observed: 
  0.272 (Depositor) 

Literature

Crystal structure of a putative Thiol:disulfide interchange protein DsbE from Chlorobium tepidum

Damodharan, L., Burley, S.K., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 67.92 kDa 
• Atom Count: 4,488 
• Modeled Residue Count: 557 
• Deposited Residue Count: 608 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative Thiol:disulfide interchange protein DsbE	A, B, C, D	152	Chlorobaculum tepidum TLS	Mutation(s): 0  Gene Names: CT1072
UniProt
Find proteins for Q8KDH8 (Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS)) Explore Q8KDH8  Go to UniProtKB:  Q8KDH8

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.296 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.263 (Depositor), 0.280 (DCC) 
• R-Value Observed: 0.272 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.197	α = 90
b = 42.067	β = 108.77
c = 82.522	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-31 
Deposition Author(s): Damodharan, L., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-03-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Structure summary