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- PDB-6d7r: Crystal structure of an inactivate variant of the quorum-sensing ... -

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Basic information

Entry
Database: PDB / ID: 6d7r
TitleCrystal structure of an inactivate variant of the quorum-sensing master regulator HapR from protease-deficient non-O1, non-O139 Vibrio cholerae strain V2
ComponentsHemagglutinin/protease regulatory protein
KeywordsTRANSCRIPTION / TetR / quorum-sensing
Function / homology
Function and homology information


peptidase activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / proteolysis
Similarity search - Function
: / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Hemagglutinin/protease regulatory protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCruite, J.T. / Succo, P. / Raychaudhuri, S. / Kull, F.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI072661-10 United States
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystal structure of an inactive variant of the quorum-sensing master regulator HapR from the protease-deficient non-O1, non-O139 Vibrio cholerae strain V2.
Authors: Cruite, J. / Succo, P. / Raychaudhuri, S. / Kull, F.J.
History
DepositionApr 25, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionMay 30, 2018ID: 5L0X
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 27, 2022Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemagglutinin/protease regulatory protein
B: Hemagglutinin/protease regulatory protein


Theoretical massNumber of molelcules
Total (without water)51,9042
Polymers51,9042
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-16 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.470, 85.710, 112.250
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 Hemagglutinin/protease regulatory protein / LuxR family transcriptional regulator


Mass: 25951.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: hapR, BTY66_11620, EN12_02415, ERS013138_01392, ERS013140_02369, ERS013173_01523, ERS013186_00946, ERS013193_02550, ERS013198_01284, ERS013202_02486
Production host: Escherichia coli (E. coli) / References: UniProt: B2CKP3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.01 Å3/Da / Density % sol: 38.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 15% PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→19.428 Å / Num. obs: 182643 / % possible obs: 99.8 % / Redundancy: 7.2 % / CC1/2: 0.999 / Net I/σ(I): 19.04
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.08 / Num. unique obs: 2496 / CC1/2: 0.745 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
PHASERphasing
PHENIX(1.12_2829)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PBX

2pbx


Resolution: 2.1→19.428 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.4
RfactorNum. reflection% reflection
Rfree0.268 3727 7.89 %
Rwork0.2025 --
obs0.2077 47226 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3246 0 0 79 3325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083313
X-RAY DIFFRACTIONf_angle_d0.9264478
X-RAY DIFFRACTIONf_dihedral_angle_d2.9911996
X-RAY DIFFRACTIONf_chiral_restr0.045500
X-RAY DIFFRACTIONf_plane_restr0.006570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12660.39681390.31261590X-RAY DIFFRACTION100
2.1266-2.15450.36121410.31631640X-RAY DIFFRACTION100
2.1545-2.1840.32491480.29591659X-RAY DIFFRACTION100
2.184-2.21520.26481320.27561544X-RAY DIFFRACTION100
2.2152-2.24820.33261350.29991598X-RAY DIFFRACTION100
2.2482-2.28330.34711400.26851638X-RAY DIFFRACTION100
2.2833-2.32060.29461380.25881597X-RAY DIFFRACTION100
2.3206-2.36060.34051370.24511610X-RAY DIFFRACTION100
2.3606-2.40340.31921450.25811656X-RAY DIFFRACTION100
2.4034-2.44960.30441350.23621564X-RAY DIFFRACTION100
2.4496-2.49950.31071370.22741605X-RAY DIFFRACTION100
2.4995-2.55370.27031480.22311667X-RAY DIFFRACTION100
2.5537-2.6130.32351350.21631561X-RAY DIFFRACTION100
2.613-2.67820.32451380.22031628X-RAY DIFFRACTION100
2.6782-2.75040.31521390.22441604X-RAY DIFFRACTION100
2.7504-2.83110.3321360.20751594X-RAY DIFFRACTION100
2.8311-2.92220.35431360.2171625X-RAY DIFFRACTION100
2.9222-3.02620.28451330.21861598X-RAY DIFFRACTION100
3.0262-3.14690.27691470.20621619X-RAY DIFFRACTION100
3.1469-3.28950.30381350.20951613X-RAY DIFFRACTION100
3.2895-3.4620.27931390.20071609X-RAY DIFFRACTION100
3.462-3.67750.29521330.18371609X-RAY DIFFRACTION100
3.6775-3.95930.29661370.17971623X-RAY DIFFRACTION100
3.9593-4.35360.17351370.16791629X-RAY DIFFRACTION100
4.3536-4.97440.22131330.15811592X-RAY DIFFRACTION100
4.9744-6.23260.22531390.19781618X-RAY DIFFRACTION100
6.2326-19.4280.18191350.1591609X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -10.5448 Å / Origin y: -1.0746 Å / Origin z: 17.2118 Å
111213212223313233
T0.1785 Å2-0.0028 Å20.0179 Å2-0.2415 Å2-0.0093 Å2--0.2187 Å2
L0.4567 °2-0.4313 °2-0.0804 °2-1.4846 °20.2686 °2--0.507 °2
S0.0235 Å °-0.0648 Å °0.0536 Å °-0.0663 Å °0.031 Å °-0.0591 Å °0.0379 Å °0.0901 Å °0.0001 Å °
Refinement TLS groupSelection details: all

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