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- PDB-5dbk: apo form of the quorum sensor NprR from B. thuringiensis -

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Basic information

Entry
Database: PDB / ID: 5dbk
Titleapo form of the quorum sensor NprR from B. thuringiensis
ComponentsTranscriptional regulator/TPR domain protein
KeywordsSIGNALING PROTEIN / truncated form / TPR domain / mutant protein / asymmetric dimer
Function / homology
Function and homology information


Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #1000 / : / 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 / TPR repeat region circular profile. / TPR repeat profile. ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #1000 / : / 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 / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator/TPR domain protein
Similarity search - Component
Biological speciesBacillus thuringiensis Bt407 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.241 Å
AuthorsTalagas, A. / Perchat, S. / Lereclus, D. / Nessler, S.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyNT09_443605 France
CitationJournal: Plos Pathog. / Year: 2016
Title: How Quorum Sensing Connects Sporulation to Necrotrophism in Bacillus thuringiensis.
Authors: Perchat, S. / Talagas, A. / Poncet, S. / Lazar, N. / Li de la Sierra-Gallay, I. / Gohar, M. / Lereclus, D. / Nessler, S.
History
DepositionAug 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 8, 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

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Assembly

Deposited unit
A: Transcriptional regulator/TPR domain protein
B: Transcriptional regulator/TPR domain protein


Theoretical massNumber of molelcules
Total (without water)88,7262
Polymers88,7262
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-19 kcal/mol
Surface area35380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.789, 105.337, 177.068
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transcriptional regulator/TPR domain protein


Mass: 44363.031 Da / Num. of mol.: 2 / Fragment: RESIDUES 13-375 / Mutation: Y223A, F225A
Source method: isolated from a genetically manipulated source
Details: THIS IS A TRUNCATED FORM OF THE PROTEIN, MISSING THE 60 RESIDUES OF THE N-TERMINAL HTH DOMAIN, WITH A C-TERMINAL HIS-TAG
Source: (gene. exp.) Bacillus thuringiensis Bt407 (bacteria)
Gene: nprR / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Variant (production host): M15 [pRep4] / References: UniProt: M1Q3P9

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 65.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.6
Details: NA CITRATE 1.0 M, HEPES 100 MM, PH 7.6, VAPOR DIFFUSION, TEMPERATURE 291K
PH range: 7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 25, 2013
RadiationMonochromator: SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.24→50 Å / Num. obs: 20499 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.46 % / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 10.03
Reflection shellResolution: 3.24→3.44 Å / Redundancy: 3.53 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.18 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 3.241→47.929 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2447 1025 5 %
Rwork0.2112 --
obs0.2129 20489 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.241→47.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5921 0 0 0 5921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026033
X-RAY DIFFRACTIONf_angle_d0.5288108
X-RAY DIFFRACTIONf_dihedral_angle_d11.8012308
X-RAY DIFFRACTIONf_chiral_restr0.021878
X-RAY DIFFRACTIONf_plane_restr0.0011011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2411-3.41190.33511380.30592634X-RAY DIFFRACTION95
3.4119-3.62560.33261450.25182747X-RAY DIFFRACTION99
3.6256-3.90540.25871450.24022745X-RAY DIFFRACTION99
3.9054-4.29820.261470.19882794X-RAY DIFFRACTION100
4.2982-4.91960.23171450.19272772X-RAY DIFFRACTION98
4.9196-6.19610.27281490.23382823X-RAY DIFFRACTION99
6.1961-47.93420.18231560.17372949X-RAY DIFFRACTION99

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