3CFY | pdb_00003cfy

Crystal structure of signal receiver domain of putative Luxo repressor protein from Vibrio parahaemolyticus

PDB DOI: https://doi.org/10.2210/pdb3CFY/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Vibrio parahaemolyticus RIMD 2210633
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-03-04 Released: 2008-03-18
Deposition Author(s): Patskovsky, Y., Ramagopal, U.A., Fong, R., Freeman, J., Iizuka, M., Groshong, C., Smith, D., Wasserman, S.R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.291 (Depositor), 0.283 (DCC)
R-Value Work:
0.246 (Depositor), 0.243 (DCC)
R-Value Observed:
0.248 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of Signal Receiver Domain of Putative Luxo Repressor Protein from Vibrio Parahaemolyticus.

Patskovsky, Y., Ramagopal, U.A., Fong, R., Freeman, J., Iizuka, M., Groshong, C., Smith, D., Wasserman, S.R., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 15.6 kDa
Atom Count: 1,061
Modeled Residue Count: 130
Deposited Residue Count: 137
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative LuxO repressor protein	A	137	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 0 Gene Names: VP1469
UniProt
Find proteins for Q87PN2 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87PN2 Go to UniProtKB: Q87PN2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q87PN2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.291 (Depositor), 0.283 (DCC)
R-Value Work: 0.246 (Depositor), 0.243 (DCC)
R-Value Observed: 0.248 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.203	α = 90
b = 58.203	β = 90
c = 96.692	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-03-18

Deposition Author(s):

Ramagopal, U.A.

Wasserman, S.R.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-03-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2018-11-14
Changes: Data collection, Structure summary
Version 1.4: 2021-02-03
Changes: Database references, Structure summary
Version 1.5: 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.