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- PDB-1omi: Crystal structure of PrfA,the transcriptional regulator in Lister... -

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Basic information

Entry
Database: PDB / ID: 1omi
TitleCrystal structure of PrfA,the transcriptional regulator in Listeria monocytogenes
ComponentsListeriolysin regulatory protein
KeywordsTRANSCRIPTION / Transcriptional regulator PrfA / CAP fold / LISTERIA MONOCYTOGENES / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytosol
Similarity search - Function
Single helix bin / Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single helix bin / Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Listeriolysin regulatory protein
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsThirumuruhan, 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)
Citation
Journal: To be Published
Title: Crystal structure of PrfA, the transcriptional regulator in Listeria monocytogenes
Authors: Thirumuruhan, R. / Rajashankar, K. / Fedorov, A.A. / Dodatko, T. / Chance, M.R. / Cossart, P. / Almo, S.C.
#1: Journal: Int.J.Med.Microbiol. / Year: 2002
Title: Molecular and cellular basis of the infection by Listeria monocytogenes: an overview
Authors: Cossart, P.
#2: Journal: Mol.Microbiol. / Year: 1996
Title: A single subsitution in the putative helix-turn-helix motif of the pleiotropic activator PrfA attenuates Listeria monocytogenes virulance
Authors: Sheehan, B. / Klarsfeld, A. / Ebright, R. / Cossart, P.
History
DepositionFeb 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_ref_seq_dif.details ..._audit_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Listeriolysin regulatory protein
B: Listeriolysin regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8814
Polymers56,6972
Non-polymers1842
Water00
1
A: Listeriolysin regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4412
Polymers28,3491
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Listeriolysin regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4412
Polymers28,3491
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-37 kcal/mol
Surface area20270 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)69.430, 72.091, 114.335
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer

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Components

#1: Protein Listeriolysin regulatory protein


Mass: 28348.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: PRFA OR LMO0200 / Production host: Escherichia coli (E. coli) / References: UniProt: P22262
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.622 Å3/Da / Density % sol: 51.29 %
Crystal growTemperature: 319 K / Method: vapor diffusion / pH: 8.5
Details: 20% ethanol, 0.1M tris HCl, pH 8.5, VAPOR DIFFUSION, temperature 319K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 10, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 16444 / Num. obs: 16444 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Biso Wilson estimate: 68 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 28.6
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 7.2 / % possible all: 95.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.8→20 Å / Rfactor Rfree error: 0.01 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 701 4.9 %RANDOM
Rwork0.244 ---
obs0.248 14309 97.7 %-
all-14309 --
Solvent computationSolvent model: flat model / Bsol: 35.9697 Å2 / ksol: 0.309603 e/Å3
Displacement parametersBiso mean: 76.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.79 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3688 0 12 0 3700
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it3.071.5
X-RAY DIFFRACTIONc_mcangle_it5.042
X-RAY DIFFRACTIONc_scbond_it3.972
X-RAY DIFFRACTIONc_scangle_it6.642.5
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.069 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.49 61 4.5 %
Rwork0.43 1155 -
obs-1364 84.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4gol_xplor_par.txtgol_xplor_top.txt

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