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- PDB-2bgc: PrfA-G145S, a constitutive active mutant of the Transcriptional R... -

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Basic information

Entry
Database: PDB / ID: 2bgc
TitlePrfA-G145S, a constitutive active mutant of the Transcriptional Regulator In L.monocytogenes
ComponentsPRFA
KeywordsTRANSCRIPTION / BACTERIAL INFECTION / HUMAN PATHOGEN / TRANSCRIPTIONAL REGULATOR
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-type HTH domain profile. / Crp-like helix-turn-helix domain / 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-type HTH domain profile. / Crp-like helix-turn-helix domain / 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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Listeriolysin regulatory protein
Similarity search - Component
Biological speciesLISTERIA MONOCYTOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionDec 20, 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 / Derived calculations / 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_conn
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_conn.pdbx_leaving_atom_flag
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PRFA
B: PRFA
D: PRFA
E: PRFA
F: PRFA
G: PRFA
H: PRFA
I: PRFA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,75310
Polymers219,4448
Non-polymers3092
Water7,008389
1
A: PRFA
B: PRFA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0153
Polymers54,8612
Non-polymers1541
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: PRFA
E: PRFA


Theoretical massNumber of molelcules
Total (without water)54,8612
Polymers54,8612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
F: PRFA
G: PRFA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0153
Polymers54,8612
Non-polymers1541
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
H: PRFA
I: PRFA


Theoretical massNumber of molelcules
Total (without water)54,8612
Polymers54,8612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)117.247, 100.243, 189.563
Angle α, β, γ (deg.)90.00, 90.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
PRFA


Mass: 27430.500 Da / Num. of mol.: 8 / Mutation: YES
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
#2: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Dithioerythritol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: POSITIVE REGULATION OF THE EXPRESSION OF LISTERIOLYSIN, OF 1-PHOSPHADIDYLINOSITOL ...FUNCTION: POSITIVE REGULATION OF THE EXPRESSION OF LISTERIOLYSIN, OF 1-PHOSPHADIDYLINOSITOL PHOSPHODIESTERASE (PI-PLC) AND OTHER VIRULENCE FACTORS ENGINEERED MUTATION IN CHAINS A, B, D, E, F, G, H, I GLY 145 TO SER
Sequence detailsTHE PRFA-CONSTRUCTS WERE DESIGNED WITH AN N-TERMINAL HIS-TAG. THEREFORE THE CLONING SEQUENCE STARTS ...THE PRFA-CONSTRUCTS WERE DESIGNED WITH AN N-TERMINAL HIS-TAG. THEREFORE THE CLONING SEQUENCE STARTS WITH GLY-SER

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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: 2.54 Å3/Da / Density % sol: 51.25 %
Crystal growpH: 6.9
Details: 12 % (W/V) PEG 8000 100 MM NA-MES PH 6.9 300 MM NA-ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 21, 2003 / Details: MIRRORS
RadiationMonochromator: DOUBLE-CRYSTAL SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 89772 / % possible obs: 92.3 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Net I/σ(I): 13
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.03 / Mean I/σ(I) obs: 2.5 / % possible all: 94.1

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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: 2.3→182.57 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.914 / SU B: 17.311 / SU ML: 0.207 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.361 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.268 4648 5 %RANDOM
Rwork0.195 ---
obs0.199 88472 95.6 %-
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: 47.74 Å2
Baniso -1Baniso -2Baniso -3
1-4.5 Å20 Å2-0.04 Å2
2---2.58 Å20 Å2
3----1.92 Å2
Refinement stepCycle: LAST / Resolution: 2.3→182.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15239 0 16 389 15644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02215599
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213878
X-RAY DIFFRACTIONr_angle_refined_deg1.7391.96321067
X-RAY DIFFRACTIONr_angle_other_deg0.908332538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.15951857
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.76925.391703
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.699152845
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1391516
X-RAY DIFFRACTIONr_chiral_restr0.1010.22327
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216963
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023133
X-RAY DIFFRACTIONr_nbd_refined0.2140.23002
X-RAY DIFFRACTIONr_nbd_other0.1760.212571
X-RAY DIFFRACTIONr_nbtor_refined0.1850.27175
X-RAY DIFFRACTIONr_nbtor_other0.0890.28209
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2478
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0570.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.25429753
X-RAY DIFFRACTIONr_mcbond_other0.5423811
X-RAY DIFFRACTIONr_mcangle_it3.302315009
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.96827176
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.91236058
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
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 335 -
Rwork0.261 6505 -
obs--96.82 %
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)
10.8067-0.0252-0.31992.59310.59540.7658-0.011-0.0374-0.0278-0.5681-0.2560.5482-0.1938-0.03370.26690.00470.0456-0.187-0.0765-0.07970.044114.409189.364861.391
23.7264-1.7833-0.97193.83771.88133.2534-0.3406-0.2107-0.62760.6534-0.41861.23670.501-0.6360.7592-0.1816-0.14060.22290.0002-0.10570.35794.249475.258578.0981
30.6509-0.0180.52091.27160.3540.89710.0070.00230.02950.0168-0.0176-0.0429-0.00190.11370.0106-0.0586-0.00580.0011-0.00160.0098-0.055132.7588.693576.2954
41.0975-0.22551.05413.1313-0.07171.65550.14010.1378-0.05270.04240.0585-0.11810.17040.2315-0.1986-0.01460.0534-0.0316-0.0509-0.0373-0.067635.382666.283367.9667
51.54690.3718-0.4730.8150.03931.90410.01790.0399-0.1618-0.02080.0830.00170.2042-0.2772-0.1009-0.0977-0.0295-0.0277-0.01860.0146-0.015914.864459.121715.4925
69.848-1.3997-4.6391.9196-0.33444.4806-0.3389-0.0373-0.63460.0373-0.14190.3628-0.102-0.29450.4808-0.24410.08570.08110.101-0.0733-0.04442.926868.646434.9161
70.72350.32260.10040.8842-0.32891.69650.01640.0808-0.04130.06930.0177-0.0209-0.16470.064-0.0341-0.0582-0.00180.0037-0.0277-0.0133-0.053229.775176.840219.1741
81.0130.1844-0.02090.9397-0.16962.0012-0.1194-0.0757-0.0988-0.06010.0777-0.1507-0.13370.13590.04170.0024-0.02660.0095-0.0374-0.0055-0.073836.615164.11738.4806
90.92420.15550.15182.50190.58570.85730.00080.03640.03910.5391-0.24830.48690.2073-0.09550.2475-0.0042-0.05450.1626-0.0556-0.08970.032914.584211.063833.4366
102.89131.62030.76973.0141.33412.8182-0.4030.25650.5729-0.5314-0.28081.1222-0.3562-0.65150.6838-0.21030.1307-0.24250.0149-0.10030.36734.491925.032716.6735
110.6706-0.0483-0.41751.43940.3240.91930.02480.0038-0.0343-0.0331-0.0314-0.0602-0.01730.11340.0066-0.0572-0.00340.01040.00580.002-0.06833.11311.670518.5358
120.79370.2128-1.02832.6337-0.10282.0230.1364-0.1570.0229-0.06160.0544-0.1072-0.17890.2572-0.1908-0.0157-0.04970.0312-0.0278-0.0382-0.062335.619534.003926.8199
131.6561-0.47010.17330.9504-0.19341.72940.0263-0.03750.17970.01120.06090.0267-0.1888-0.2724-0.0873-0.08430.02210.0292-0.01880.0176-0.036414.493141.206879.2749
1412.10860.46593.40944.01150.05812.9425-0.20510.26170.6418-0.0228-0.27770.40960.2533-0.54320.4828-0.2424-0.0749-0.0930.0569-0.0475-0.03022.84931.709759.7087
150.5895-0.2863-0.00320.7069-0.33231.66350.0338-0.10850.0113-0.0870.0339-0.00870.20380.0279-0.0677-0.0441-0.00290.0049-0.0187-0.0091-0.050229.466323.523575.6047
160.5442-0.31630.36621.17850.18551.8823-0.15040.10370.0870.06230.0491-0.17180.19240.09340.1013-0.00190.01530.0006-0.02020.0069-0.066536.494236.26656.2933
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 138
2X-RAY DIFFRACTION2A139 - 237
3X-RAY DIFFRACTION3B2 - 138
4X-RAY DIFFRACTION4B139 - 237
5X-RAY DIFFRACTION5D3 - 138
6X-RAY DIFFRACTION6D139 - 237
7X-RAY DIFFRACTION7E2 - 138
8X-RAY DIFFRACTION8E139 - 237
9X-RAY DIFFRACTION9F2 - 138
10X-RAY DIFFRACTION10F139 - 237
11X-RAY DIFFRACTION11G3 - 138
12X-RAY DIFFRACTION12G139 - 237
13X-RAY DIFFRACTION13H3 - 138
14X-RAY DIFFRACTION14H139 - 235
15X-RAY DIFFRACTION15I2 - 138
16X-RAY DIFFRACTION16I139 - 237

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