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- PDB-2beo: PrfA, Transcriptional Regulator In Listeria Monocytogenes -

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Basic information

Entry
Database: PDB / ID: 2beo
TitlePrfA, Transcriptional Regulator In Listeria Monocytogenes
ComponentsLISTERIOLYSIN REGULATORY PROTEIN
KeywordsTRANSCRIPTION / BACTERIAL INFECTION / HUMAN PATHOGEN / TRANSCRIPTIONAL REGULATOR / ACTIVATOR / VIRULENCE
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytosol
Similarity search - Function
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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...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 / 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 / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACETAMIDE / GLUTAMINE / Listeriolysin regulatory protein
Similarity search - Component
Biological speciesLISTERIA MONOCYTOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsEiting, M. / Hagelueken, G. / Schubert, W.-D. / Heinz, D.W.
CitationJournal: Mol.Microbiol. / Year: 2005
Title: The Mutation G145S in Prfa, a Key Virulence Regulator of Listeria Monocytogenes, Increases DNA-Binding Affinity by Stabilizing the Hth Motif
Authors: Eiting, M. / Hagelueken, G. / Schubert, W.-D. / Heinz, D.W.
History
DepositionNov 26, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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)54,8677
Polymers54,3962
Non-polymers4705
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.951, 80.713, 60.965
Angle α, β, γ (deg.)90.00, 111.91, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNILEILE2AA4 - 993 - 98
21GLNGLNILEILE2BB4 - 993 - 98
12ASNASNILEILE1AA109 - 136108 - 135
22ASNASNILEILE1BB109 - 136108 - 135
13ASNASNMETMET3AA137 - 171136 - 170
23ASNASNMETMET3BB137 - 171136 - 170
14ILEILEASNASN3AA189 - 210188 - 209
24ILEILEASNASN3BB189 - 210188 - 209

NCS oper: (Code: given
Matrix: (0.24412, -0.86544, 0.43752), (-0.85231, -0.40669, -0.32891), (0.46258, -0.29261, -0.8369)
Vector: 85.71336, 124.25512, 1.14282)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein LISTERIOLYSIN REGULATORY PROTEIN / PRFA


Mass: 27198.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Strain: EGD-E / Plasmid: PQE-30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: P22262

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Non-polymers , 5 types, 44 molecules

#2: Chemical ChemComp-GLN / GLUTAMINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-ACM / ACETAMIDE


Mass: 59.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsFUNCTION: POSITIVELY REGULATES EXPRESSION OF LISTERIOLYSIN AND OTHER VIRULENCE FACTORS.

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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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growpH: 6.5
Details: 20 % (W/V) PEG 6000 100 MM NA-MES PH6.5 1 M LICL, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 15, 2003 / Details: RH-COATED SILICON MIRROR
RadiationMonochromator: DOUBLE SI-111 CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 12402 / % possible obs: 89 % / Observed criterion σ(I): 1 / Redundancy: 1.76 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 10.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.03 / Mean I/σ(I) obs: 3.1 / % possible all: 68.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OMI

1omi


Resolution: 2.7→56.8 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.882 / SU ML: 0.413 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.478 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.289 602 4.9 %RANDOM
Rwork0.244 ---
obs0.246 11790 91.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.92 Å2
Baniso -1Baniso -2Baniso -3
1-4.66 Å20 Å28.23 Å2
2---2.29 Å20 Å2
3---3.76 Å2
Refinement stepCycle: LAST / Resolution: 2.7→56.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3740 0 27 39 3806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224098
X-RAY DIFFRACTIONr_bond_other_d0.0040.023616
X-RAY DIFFRACTIONr_angle_refined_deg1.9441.9595563
X-RAY DIFFRACTIONr_angle_other_deg1.38238510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4335502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82325.579190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.85415755
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.653154
X-RAY DIFFRACTIONr_chiral_restr0.1450.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024580
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02830
X-RAY DIFFRACTIONr_nbd_refined0.1930.2906
X-RAY DIFFRACTIONr_nbd_other0.1620.23507
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21943
X-RAY DIFFRACTIONr_nbtor_other0.0840.22150
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.293
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1830.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.28822530
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.22433960
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.50121864
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.61631603
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1188tight positional0.040.05
834medium positional0.650.5
460loose positional0.885
1188tight thermal0.030.5
834medium thermal0.222
460loose thermal1.1110
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.332 39
Rwork0.329 661
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.61630.30460.44623.6756-0.54460.62220.0185-0.148-0.06920.21280.08620.29820.0766-0.0182-0.10480.246-0.0029-0.29420.1053-0.0040.43729.11961.8186.677
24.95-0.5307-1.73244.5293-2.02374.58330.1864-1.3684-0.46740.9319-0.3999-0.14870.50130.68660.21350.6687-0.082-0.46120.5240.07450.57748.79964.88721.053
32.564-0.2623-0.34282.7919-0.01161.240.11840.40350.2346-0.6414-0.1053-0.274-0.03310.1839-0.0130.35780.0462-0.26660.22350.03310.466642.11972.777-8.912
46.976-3.6971-0.25276.8637-0.12370.61840.33850.51930.2851-0.9035-0.4491-0.5121-0.20180.2310.11060.49580.1352-0.23830.27970.03930.401950.81850.087-13.284
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 137
2X-RAY DIFFRACTION2A138 - 237
3X-RAY DIFFRACTION3B3 - 137
4X-RAY DIFFRACTION4B138 - 237

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