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- PDB-7xxt: HapR Quadruple mutant, bound to IMTVC-212 -

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Basic information

Entry
Database: PDB / ID: 7xxt
TitleHapR Quadruple mutant, bound to IMTVC-212
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
1-((5-phenylthiophen-2-yl)sulfonyl)-1H-pyrazole / Hemagglutinin/protease regulatory protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.501 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
Revision 1.2Oct 9, 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)24,0173
Polymers23,6481
Non-polymers3682
Water59433
1
A: Hemagglutinin/protease regulatory protein
hetero molecules

A: Hemagglutinin/protease regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0346
Polymers47,2972
Non-polymers7374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3390 Å2
ΔGint-7 kcal/mol
Surface area18460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.987, 44.953, 53.573
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: 23648.334 Da / Num. of mol.: 1 / Mutation: Y76F, L97I, I141V, 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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-7PI / 1-((5-phenylthiophen-2-yl)sulfonyl)-1H-pyrazole / IMTVC-212


Mass: 290.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H10N2O2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 7-8% 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: Feb 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.49→27.35 Å / Num. obs: 14492 / % possible obs: 99.1 % / Redundancy: 9.1 % / CC1/2: 0.99 / Net I/σ(I): 12.6
Reflection shellResolution: 2.49→2.58 Å / Num. unique obs: 693 / CC1/2: 0.9 / % possible all: 90.8

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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: 2.501→26.786 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2589 1445 10 %
Rwork0.2053 13005 -
obs0.2106 14450 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.12 Å2 / Biso mean: 45.6985 Å2 / Biso min: 18.23 Å2
Refinement stepCycle: final / Resolution: 2.501→26.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1620 0 23 33 1676
Biso mean--46.62 36.35 -
Num. residues----198
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.51-2.59010.35031380.2776127598
2.5901-2.69370.39431470.26621300100
2.6937-2.81620.25871490.24231329100
2.8162-2.96450.33371400.251290100
2.9645-3.14990.31821400.23171293100
3.1499-3.39270.29191450.2261285100
3.3927-3.73330.2611510.21081327100
3.7333-4.27170.20741430.16691283100
4.2717-5.37470.22391510.16771324100
5.3747-26.780.20511410.18161299100
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)
10.91190.6173-0.80740.7343-0.84771.05850.11490.4292-0.28030.18870.4881-0.52590.1713-0.06050.11990.3972-0.0056-0.03960.2596-0.13250.326122.21612.409632.3909
20.33540.24650.50410.97041.14431.32480.03690.03760.04780.1188-0.06190.007-0.0214-0.36770.00450.1968-0.0623-0.01210.2772-0.00180.276316.09088.669229.9502
30.45010.5048-0.11040.71540.15880.544500.0423-0.13120.065-0.2625-0.2776-0.15450.6443-0.00020.1918-0.0170.03510.33430.02730.232415.79312.13144.048
40.13130.12260.18210.5054-0.16510.5795-0.0336-0.26350.04630.1423-0.21650.066-0.1104-0.1311-0.00170.263-0.0507-0.01180.2637-0.03080.28755.41447.772920.338
50.244-0.0383-0.06130.38870.56472.27540.36280.13250.3523-0.17370.2961-0.1726-0.23120.52530.10930.3163-0.00420.04720.21360.00520.30856.659113.9265-1.0767
61.77920.2049-0.36120.88550.65750.6946-0.0048-0.023-0.2693-0.1868-0.04340.04350.13250.14550.00140.28450.0210.02310.2295-0.00610.2996.4315-2.59255.4676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 33 )A5 - 33
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 83 )A34 - 83
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 107 )A84 - 107
4X-RAY DIFFRACTION4chain 'A' and (resid 108 through 134 )A108 - 134
5X-RAY DIFFRACTION5chain 'A' and (resid 135 through 159 )A135 - 159
6X-RAY DIFFRACTION6chain 'A' and (resid 160 through 202 )A160 - 202

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