1OMI | pdb_00001omi

Crystal structure of PrfA,the transcriptional regulator in Listeria monocytogenes

PDB DOI: https://doi.org/10.2210/pdb1OMI/pdb

Classification: TRANSCRIPTION
Organism(s): Listeria monocytogenes
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2003-02-25 Released: 2003-03-11
Deposition Author(s): Thirumuruhan, R., Rajashankar, K., Fedorov, A.A., Dodatko, T., Chance, M.R., Cossart, P., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.278 (Depositor), 0.275 (DCC)
R-Value Work:
0.244 (Depositor), 0.243 (DCC)
R-Value Observed:
0.248 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1OMI

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

Literature

Crystal structure of PrfA, the transcriptional regulator in Listeria monocytogenes

Thirumuruhan, R., Rajashankar, K., Fedorov, A.A., Dodatko, T., Chance, M.R., Cossart, P., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 56.88 kDa
Atom Count: 3,700
Modeled Residue Count: 451
Deposited Residue Count: 496
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Listeriolysin regulatory protein	A, B	248	Listeria monocytogenes	Mutation(s): 0 Gene Names: PRFA OR LMO0200
UniProt
Find proteins for P22262 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore P22262 Go to UniProtKB: P22262
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22262
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.278 (Depositor), 0.275 (DCC)
R-Value Work: 0.244 (Depositor), 0.243 (DCC)
R-Value Observed: 0.248 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.43	α = 90
b = 72.091	β = 90
c = 114.335	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
CNS	refinement

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2003-03-11

Deposition Author(s):

Thirumuruhan, R.

Rajashankar, K.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2003-03-11
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-02-14
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.