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- PDB-7xxo: HapR Native in CHES buffer pH 9.5 -

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Basic information

Entry
Database: PDB / ID: 7xxo
TitleHapR Native in CHES buffer pH 9.5
ComponentsHemagglutinin/protease regulatory protein
KeywordsTRANSCRIPTION / HapR Master Regulator
Function / homology
Function and homology information


peptidase activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / proteolysis
Similarity search - Function
: / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
Hemagglutinin/protease regulatory protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.487 Å
AuthorsBasu Choudhury, G. / Chaudhari, V. / Ray Chaudhuri, S. / Datta, S.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR) India
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Diversity in the ligand binding pocket of HapR attributes to its uniqueness towards several inhibitors with respect to other homologues - A structural and molecular perspective.
Authors: Sen, H. / Choudhury, G.B. / Pawar, G. / Sharma, Y. / Bhalerao, S.E. / Chaudhari, V.D. / Datta, S. / Raychaudhuri, S.
History
DepositionMay 30, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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)47,4452
Polymers47,4452
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-16 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.935, 85.399, 110.432
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hemagglutinin/protease regulatory protein / TetR/AcrR family transcriptional regulator


Mass: 23722.393 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: hapR, D6U24_16025, ERS013186_00946, ERS013198_01284, ERS013202_02486
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: B2CKP3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 7% PEG 8000, 100 mM CHES pH 9.5, 200 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Jul 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.48→26 Å / Num. obs: 15058 / % possible obs: 98.8 % / Redundancy: 7 % / CC1/2: 0.98 / Net I/σ(I): 9
Reflection shellResolution: 2.48→2.6 Å / Num. unique obs: 15000 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PBX

2pbx


Resolution: 2.487→23.89 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2679 1502 9.98 %
Rwork0.2173 13547 -
obs0.2226 15049 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.08 Å2 / Biso mean: 48.49 Å2 / Biso min: 14.28 Å2
Refinement stepCycle: final / Resolution: 2.487→23.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3233 0 0 76 3309
Biso mean---49.37 -
Num. residues----394
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.49-2.56690.32851200.2831108488
2.5669-2.65850.32531360.26941223100
2.6585-2.76480.31111340.26191226100
2.7648-2.89050.31881350.25821208100
2.8905-3.04260.31061360.24891227100
3.0426-3.23280.28991350.23561220100
3.2328-3.48170.31881400.2391243100
3.4817-3.83080.28681380.2071255100
3.8308-4.38210.23991390.18341249100
4.3821-5.50980.21891420.18921272100
5.5098-100.21651470.19671340100

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