3D3R

Crystal structure of the hydrogenase assembly chaperone HypC/HupF family protein from Shewanella oneidensis MR-1

• PDB DOI: https://doi.org/10.2210/pdb3D3R/pdb

• Classification: CHAPERONE
• Organism(s): Shewanella oneidensis MR-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-12 Released: 2008-05-27 
• Deposition Author(s): Kim, Y., Skarina, T., Onopriyenko, O., Edwards, A.M., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.234 
• R-Value Work: 0.202 
• R-Value Observed: 0.203 

Literature

Crystal Structure of the Hydrogenase Assembly Chaperone HypC/HupF Family Protein from Shewanella oneidensis MR-1.

Kim, Y., Skarina, T., Onopriyenko, O., Edwards, A.M., Savchenko, A., Joachimiak, A.

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)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 23.46 kDa 
• Atom Count: 1,421 
• Modelled Residue Count: 163 
• Deposited Residue Count: 206 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydrogenase assembly chaperone hypC/hupF	A, B	103	Shewanella oneidensis MR-1	Mutation(s): 0  Gene Names: hypC, SO_2092
UniProt
Find proteins for Q8EF93 (Shewanella oneidensis (strain MR-1)) Explore Q8EF93  Go to UniProtKB:  Q8EF93

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.234 
• R-Value Work: 0.202 
• R-Value Observed: 0.203 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.864	α = 90
b = 58.316	β = 127.89
c = 51.924	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXD	phasing
RESOLVE	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-27 
Deposition Author(s): Kim, Y., Skarina, T., Onopriyenko, O., Edwards, A.M., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-05-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance