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- PDB-7xxn: HapR Quadruple mutant, bound to Qstatin -

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Basic information

Entry
Database: PDB / ID: 7xxn
TitleHapR Quadruple mutant, bound to Qstatin
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-bromanylthiophen-2-yl)sulfonylpyrazole / Hemagglutinin/protease regulatory protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 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 1.2Nov 13, 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)24,0343
Polymers23,6481
Non-polymers3852
Water61334
1
A: Hemagglutinin/protease regulatory protein
hetero molecules

A: Hemagglutinin/protease regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0676
Polymers47,2972
Non-polymers7714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3740 Å2
ΔGint-13 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.638, 43.795, 53.445
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-7Y3 / 1-(5-bromanylthiophen-2-yl)sulfonylpyrazole


Mass: 293.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5BrN2O2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.32 Å3/Da / Density % sol: 47.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 7-8% PEG 8000, 100 mM 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: Feb 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.45→26.53 Å / Num. obs: 14926 / % possible obs: 99 % / Redundancy: 8.4 % / CC1/2: 0.99 / Net I/av σ(I): 11.7 / Net I/σ(I): 8.3
Reflection shellResolution: 2.45→2.52 Å / Num. unique obs: 786 / CC1/2: 0.7 / % possible all: 99.7

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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: 2.45→25.609 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2609 1493 10.01 %
Rwork0.2235 13424 -
obs0.2273 14917 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.9 Å2 / Biso mean: 52.4577 Å2 / Biso min: 12.95 Å2
Refinement stepCycle: final / Resolution: 2.45→25.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1620 0 20 34 1674
Biso mean--51.15 40.57 -
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 (%)
2.4501-2.52910.3481390.3335120599
2.5291-2.61940.34731420.30051224100
2.6194-2.72420.35611390.29321214100
2.7242-2.8480.29971400.25611219100
2.848-2.99790.30571330.27171224100
2.9979-3.18540.31300.25111226100
3.1854-3.43090.3031290.25581227100
3.4309-3.77510.27721410.23161216100
3.7751-4.31910.20271390.18381230100
4.3191-5.43310.22561360.17811210100
5.4331-25.60.19561250.17641229100
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)
10.63870.40450.92821.1371.89271.3080.07490.04190.00010.24790.0670.02410.1571-0.31150.02850.2866-0.0332-0.01750.2311-0.01790.240317.9966.34530.908
21.6424-0.0177-1.01840.82710.58381.0022-0.23760.3349-0.2505-0.0991-0.1073-0.15350.1740.6608-0.5110.1238-0.0605-0.02890.3386-0.00470.133415.6482.4943.953
30.2114-0.42280.11960.3405-0.12070.4763-0.1124-0.4372-0.16730.023-0.08980.26950.0761-0.2898-0.00720.18-0.03010.01090.2573-0.0890.31415.4177.66120.483
40.8734-0.09340.42850.07150.03350.86610.2493-0.21610.7695-0.32570.1042-0.1068-0.3316-0.4294-0.0360.4434-0.05440.09430.3491-0.03070.4518.6315.4951.631
50.22670.3071-0.00170.1742-0.1009-0.09410.085-0.08750.1669-0.0419-0.1507-0.00420.34030.0501-0.01920.218-0.018-0.00520.21620.03990.28093.3114.9653.498
61.1242-0.23410.97320.1686-0.77021.54290.18661.0608-1.2145-0.05690.12540.39140.49960.69920.05580.3290.05920.06470.2573-0.04670.34828.408-6.0322.824
71.1836-0.94930.44191.7155-0.39110.1651-0.4953-0.0177-0.021-0.2508-0.2030.21640.0796-0.1407-0.01960.2570.05110.05140.8319-0.05830.36158.9996.35310.05
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 5:83 )A5 - 83
2X-RAY DIFFRACTION2( CHAIN A AND RESID 84:107 )A84 - 107
3X-RAY DIFFRACTION3( CHAIN A AND RESID 108:134 )A108 - 134
4X-RAY DIFFRACTION4( CHAIN A AND RESID 135:151 )A135 - 151
5X-RAY DIFFRACTION5( CHAIN A AND RESID 152:178 )A152 - 178
6X-RAY DIFFRACTION6( CHAIN A AND RESID 179:202 )A179 - 202
7X-RAY DIFFRACTION7( CHAIN A AND RESID 301:301 )A301

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