3GFO | pdb_00003gfo

Structure of cbiO1 from clostridium perfringens: Part of the ABC transporter complex cbiONQ.

PDB DOI: https://doi.org/10.2210/pdb3GFO/pdb

Classification: ATP binding protein
Organism(s): Clostridium perfringens ATCC 13124
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-02-27 Released: 2009-03-24
Deposition Author(s): Ramagopal, U.A., Morano, C., Toro, R., Dickey, M., Do, J., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.263 (Depositor), 0.259 (DCC)
R-Value Work:
0.206 (Depositor), 0.204 (DCC)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structure of cbiO1 from clostridium perfringens: Part of the ABC transporter complex cbiONQ

Ramagopal, U.A., Morano, C., Toro, R., Dickey, M., Do, J., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 31.14 kDa
Atom Count: 2,008
Modeled Residue Count: 251
Deposited Residue Count: 275
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cobalt import ATP-binding protein cbiO 1	A	275	Clostridium perfringens ATCC 13124	Mutation(s): 0 Gene Names: cbiO1, CPF_0188 EC: 3.6.3 (PDB Primary Data), 7 (UniProt)
UniProt
Find proteins for Q0TUN8 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)) Explore Q0TUN8 Go to UniProtKB: Q0TUN8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q0TUN8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.263 (Depositor), 0.259 (DCC)
R-Value Work: 0.206 (Depositor), 0.204 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.701	α = 90
b = 57.578	β = 103.39
c = 41.245	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SHELXD	phasing
SHELXE	model building
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-03-24

Deposition Author(s):

Ramagopal, U.A.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-03-24
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-02-21
Changes: Data collection, Database references

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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.