3D3R | pdb_00003d3r

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.234 (Depositor), 0.233 (DCC)
R-Value Work:
0.202 (Depositor), 0.200 (DCC)
R-Value Observed:
0.203 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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 ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)) Explore Q8EF93 Go to UniProtKB: Q8EF93
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8EF93
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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 (Depositor), 0.233 (DCC)
R-Value Work: 0.202 (Depositor), 0.200 (DCC)
R-Value Observed: 0.203 (Depositor)

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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-05-27

Deposition Author(s):

Onopriyenko, O.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-05-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, 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.