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- PDB-4fsc: Crystal Structure of Bacillus thuringiensis PlcR in its apo form -

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Basic information

Entry
Database: PDB / ID: 4fsc
TitleCrystal Structure of Bacillus thuringiensis PlcR in its apo form
ComponentsTranscriptional activator PlcR protein
KeywordsTRANSCRIPTION ACTIVATOR / plcR apoform / HTH DNA-binding domain / Quorum Sensing / HTH_3 (Helix-turn-helix) domain / TPR_1 (tetratricopeptide repeats) / Pleiotropic regulator / Transcriptional activator
Function / homology
Function and homology information


PlcR, tetratricopeptide repeat / RNPP family C-terminal domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Tetratricopeptide repeat domain / Lambda repressor-like, DNA-binding domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe ...PlcR, tetratricopeptide repeat / RNPP family C-terminal domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Tetratricopeptide repeat domain / Lambda repressor-like, DNA-binding domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.65 Å
AuthorsGrenha, R. / Slamti, L. / Bouillaut, L. / Lereclus, D. / Nessler, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural basis for the activation mechanism of the PlcR virulence regulator by the quorum-sensing signal peptide PapR.
Authors: Grenha, R. / Slamti, L. / Nicaise, M. / Refes, Y. / Lereclus, D. / Nessler, S.
History
DepositionJun 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional activator PlcR protein
B: Transcriptional activator PlcR protein
C: Transcriptional activator PlcR protein
D: Transcriptional activator PlcR protein


Theoretical massNumber of molelcules
Total (without water)140,2454
Polymers140,2454
Non-polymers00
Water0
1
A: Transcriptional activator PlcR protein
D: Transcriptional activator PlcR protein


Theoretical massNumber of molelcules
Total (without water)70,1232
Polymers70,1232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-28 kcal/mol
Surface area29690 Å2
MethodPISA
2
B: Transcriptional activator PlcR protein
C: Transcriptional activator PlcR protein


Theoretical massNumber of molelcules
Total (without water)70,1232
Polymers70,1232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-28 kcal/mol
Surface area30000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.589, 99.589, 137.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Transcriptional activator PlcR protein


Mass: 35061.285 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Strain: Bt407 / Gene: bthur0002_52210, plcR / Plasmid: pET16.28 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q45782

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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: 2.81 Å3/Da / Density % sol: 56.29 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M Sodium Chloride, 0.1M tri-Sodium citrate, 40% PEG400, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2011
Details: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal
RadiationMonochromator: liquid nitrogen cooled channel-cut silicon (Si) monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 3.65→86.247 Å / Num. all: 16981 / Num. obs: 16981 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 4.6 % / Biso Wilson estimate: 121.65 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 9.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
3.65-3.854.30.5331.40.533198.9
3.85-4.084.70.322.20.32199.4
4.08-4.364.50.193.80.191100
4.36-4.714.70.1345.20.134199.9
4.71-5.164.80.1126.20.1121100
5.16-5.774.80.170.1199.9
5.77-6.664.80.0926.90.0921100
6.66-8.164.90.0896.40.089199.9
8.16-11.544.70.03715.20.0371100
11.54-53.8434.70.03610.20.036199.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.65 Å53.84 Å
Translation3.65 Å53.84 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASER2.3.0phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
MxCuBEdata collection
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QFC

2qfc


Resolution: 3.65→53.84 Å / Cor.coef. Fo:Fc: 0.7731 / Cor.coef. Fo:Fc free: 0.7661 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2763 859 5.07 %RANDOM
Rwork0.2381 ---
obs0.24 16957 99.69 %-
all-17010 --
Displacement parametersBiso mean: 73.06 Å2
Baniso -1Baniso -2Baniso -3
1--3.2592 Å20 Å20 Å2
2---3.2592 Å20 Å2
3---6.5184 Å2
Refine analyzeLuzzati coordinate error obs: 0.928 Å
Refinement stepCycle: LAST / Resolution: 3.65→53.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8866 0 0 0 8866
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0089022HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0612100HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3316SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes275HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1231HARMONIC5
X-RAY DIFFRACTIONt_it9022HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.47
X-RAY DIFFRACTIONt_other_torsion26.32
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 3.65→3.87 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2902 141 5.12 %
Rwork0.2506 2611 -
all0.2526 2752 -
obs--99.69 %

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