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- PDB-3u3w: Crystal Structure of Bacillus thuringiensis PlcR in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3u3w
TitleCrystal Structure of Bacillus thuringiensis PlcR in complex with the peptide PapR7 and DNA
Components
  • 5'-D(P*AP*TP*AP*TP*GP*AP*AP*AP*TP*AP*TP*TP*GP*CP*AP*TP*AP*G)-3'
  • 5'-D(P*CP*TP*AP*TP*GP*CP*AP*AP*TP*AP*TP*TP*TP*CP*AP*TP*AP*T)-3'
  • C-terminus heptapeptide from PapR protein
  • Transcriptional activator PlcR protein
KeywordsTRANSCRIPTION ACTIVATOR/DNA / ternary complex / PlcR-PAPR7-DNA / HTH DNA-binding domain / Quorum Sensing / HTH_3 (Helix-turn-helix) domain / TPR_1 (tetratricopeptide repeats) / Pleiotropic regulator / TRANSCRIPTION ACTIVATOR-DNA complex
Function / homology
Function and homology information


DNA binding / metal ion binding
Similarity search - Function
Bacillus PapR / Bacillus PapR protein / PlcR, tetratricopeptide repeat / RNPP family C-terminal domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) ...Bacillus PapR / Bacillus PapR protein / PlcR, tetratricopeptide repeat / RNPP family C-terminal domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / PlcR associated protein, PapR / PlcR protein
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
Bacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
DepositionOct 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional activator PlcR protein
B: Transcriptional activator PlcR protein
P: C-terminus heptapeptide from PapR protein
Q: C-terminus heptapeptide from PapR protein
Y: 5'-D(P*CP*TP*AP*TP*GP*CP*AP*AP*TP*AP*TP*TP*TP*CP*AP*TP*AP*T)-3'
Z: 5'-D(P*AP*TP*AP*TP*GP*AP*AP*AP*TP*AP*TP*TP*GP*CP*AP*TP*AP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9068
Polymers82,8266
Non-polymers802
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11310 Å2
ΔGint-100 kcal/mol
Surface area31340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.880, 71.088, 88.853
Angle α, β, γ (deg.)90.00, 115.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 2 types, 2 molecules YZ

#3: DNA chain 5'-D(P*CP*TP*AP*TP*GP*CP*AP*AP*TP*AP*TP*TP*TP*CP*AP*TP*AP*T)-3'


Mass: 5464.577 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: PlcR box from the 1-phosphatidylinositol phosphodiesterase promoter plcA
#4: DNA chain 5'-D(P*AP*TP*AP*TP*GP*AP*AP*AP*TP*AP*TP*TP*GP*CP*AP*TP*AP*G)-3'


Mass: 5562.653 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: PlcR box from the 1-phosphatidylinositol phosphodiesterase promoter plcA

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Protein / Protein/peptide , 2 types, 4 molecules ABPQ

#1: Protein Transcriptional activator PlcR protein


Mass: 35061.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Strain: Bt407 / Gene: plcR / Plasmid: pET16.28 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q45782
#2: Protein/peptide C-terminus heptapeptide from PapR protein


Mass: 837.915 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bacillus cereus (bacteria) / References: UniProt: B7IR02

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Non-polymers , 2 types, 257 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

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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: 3.06 Å3/Da / Density % sol: 59.78 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.16M Calcium Acetate, 0.08M Sodium Cacodylate, 8% PEG8000, 5% Glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97932 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 29, 2011 / Details: cylindrical grazing incidence mirror
RadiationMonochromator: liquid nitrogen cooled channel-cut silicon (Si) monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.4→80.204 Å / Num. all: 39190 / Num. obs: 38014 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 2.7 % / Biso Wilson estimate: 45.4 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.4-2.532.60.6451.155640.64597.7
2.53-2.682.80.4751.453080.47598.4
2.68-2.872.70.3551.849220.35597.1
2.87-3.12.70.2462.545540.24696.7
3.1-3.392.80.1414.342740.14198.1
3.39-3.792.80.0886.837910.08896.2
3.79-4.382.70.05710.533710.05796.5
4.38-5.372.80.04413.128340.04496.3
5.37-7.592.70.03815.421790.03895.2
7.59-53.1922.70.02818.512170.02894.2

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QFC

2qfc


Resolution: 2.4→53.192 Å / SU ML: 0.35 / σ(F): 0 / Phase error: 23.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2348 1815 5.02 %RANDOM
Rwork0.1787 ---
obs0.1816 36151 91.88 %-
all-39346 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.687 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso mean: 47.6077 Å2
Baniso -1Baniso -2Baniso -3
1-10.1832 Å2-0 Å2-7.3665 Å2
2---7.0556 Å2-0 Å2
3----3.1276 Å2
Refinement stepCycle: LAST / Resolution: 2.4→53.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4822 738 2 255 5817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075888
X-RAY DIFFRACTIONf_angle_d1.028102
X-RAY DIFFRACTIONf_dihedral_angle_d20.2552310
X-RAY DIFFRACTIONf_chiral_restr0.072864
X-RAY DIFFRACTIONf_plane_restr0.003920
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.4001-2.4650.27571190.23412365236582
2.465-2.53750.34211220.23882539253989
2.5375-2.61940.32811420.24082534253489
2.6194-2.7130.29841350.22052572257290
2.713-2.82170.25451280.2122596259691
2.8217-2.95010.29221350.20672635263592
2.9501-3.10560.26411730.19312600260092
3.1056-3.30010.25061480.17272755275596
3.3001-3.55490.22521250.1692780278095
3.5549-3.91250.22071330.16272684268494
3.9125-4.47840.1981660.14392768276896
4.4784-5.64140.19811470.15212745274595
5.6414-53.20520.20871420.18262763276393

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