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- PDB-7y4j: HapR_Triple mutant Y76F, L97I, F171C -

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Basic information

Entry
Database: PDB / ID: 7y4j
TitleHapR_Triple mutant Y76F, L97I, F171C
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: 2.69 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
DepositionJun 14, 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin/protease regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8702
Polymers23,6621
Non-polymers2071
Water36020
1
A: Hemagglutinin/protease regulatory protein
hetero molecules

A: Hemagglutinin/protease regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7394
Polymers47,3252
Non-polymers4152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3490 Å2
ΔGint-6 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.587, 43.439, 53.326
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 23662.361 Da / Num. of mol.: 1 / Mutation: Y76F,L97I,F171C
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: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 7-8% PEG 8000, 100mM CHES 9.5, 200mM 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: Jun 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.69→53.326 Å / Num. obs: 11033 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.98 / Net I/σ(I): 7
Reflection shellResolution: 2.69→2.79 Å / Num. unique obs: 588 / CC1/2: 0.55 / % possible all: 100

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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: 7XY5

7xy5


Resolution: 2.69→53.326 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2878 1097 9.96 %
Rwork0.2375 9921 -
obs0.243 11018 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.79 Å2 / Biso mean: 52.5155 Å2 / Biso min: 12.3 Å2
Refinement stepCycle: final / Resolution: 2.69→53.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1627 0 13 20 1660
Biso mean--60.37 34.14 -
Num. residues----199
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6903-2.81270.38911380.3458124499
2.8127-2.9610.3821350.3136122999
2.961-3.14650.3021350.2881243100
3.1465-3.38940.38441400.28131238100
3.3894-3.73040.26191400.22551237100
3.7304-4.270.25171410.21031235100
4.27-5.37890.24831350.19321260100
5.3789-53.320.24651330.20441235100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2120.6630.38432.83751.63822.78870.00310.0545-0.12580.1222-0.2119-0.04830.54850.38190.06720.3585-0.03860.01710.16510.03150.244818.76644.983835.1862
20.55390.59311.38582.45231.26033.8838-0.2076-0.1334-0.14780.2889-0.38690.0294-0.3131-0.50310.48340.2207-0.0374-0.08380.6610.07210.33713.936314.776712.4221
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 60)A4 - 60
2X-RAY DIFFRACTION2chain 'A' and (resid 120 through 149)A120 - 149

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