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- PDB-7xy5: HapR_Double Mutant with CHES buffer -

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Basic information

Entry
Database: PDB / ID: 7xy5
TitleHapR_Double Mutant with CHES buffer
ComponentsHemagglutinin/protease regulatory protein
KeywordsTRANSCRIPTION / HapR Master Regulator Double mutant Y76F / F171C with CHES molecule TRANSCRIPTION
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: 2.37 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 31, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8702
Polymers23,6621
Non-polymers2071
Water39622
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_565-x,-y+1,z1
Buried area3800 Å2
ΔGint-6 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.934, 44.773, 53.414
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: F171C, Y76F
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.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting 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: Mar 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.37→27.28 Å / Num. obs: 16867 / % possible obs: 99 % / Redundancy: 7 % / CC1/2: 0.99 / Net I/σ(I): 13.5
Reflection shellResolution: 2.37→2.45 Å / Num. unique obs: 893 / CC1/2: 0.83

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Processing

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

2pbx


Resolution: 2.37→26.707 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2785 1668 9.92 %
Rwork0.2308 15148 -
obs0.2355 16816 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107 Å2 / Biso mean: 43.5594 Å2 / Biso min: 15.52 Å2
Refinement stepCycle: final / Resolution: 2.37→26.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 13 22 1647
Biso mean--44.15 37.69 -
Num. residues----197
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.37-2.43970.36441360.33441269100
2.4397-2.51840.31871430.29371255100
2.5184-2.60840.31211420.27491260100
2.6084-2.71270.33531410.26431285100
2.7127-2.8360.29621360.24041268100
2.836-2.98540.29361450.24531287100
2.9854-3.17210.34961290.2404126099
3.1721-3.41660.30921400.2568122799
3.4166-3.75960.29651380.2445126898
3.7596-4.30160.32511410.2048123698
4.3016-5.41220.18541410.1849125699
5.4122-26.70.21621360.18971277100
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)
10.1399-0.1594-0.23150.29340.34240.41070.28550.1926-0.0922-0.5319-0.08540.0648-0.0161-0.36130.00140.31620.0355-0.01650.29760.00240.231517.65618.4803-5.9118
20.7241-0.00230.78340.41720.48291.39630.14350.3413-0.1424-0.13890.06440.0301-0.1010.23030.32840.26050.07820.01920.1741-0.00040.235820.419312.2214-13.1407
30.3819-0.39270.40890.4219-0.13342.4541-0.0545-0.02450.20610.0477-0.1215-0.11550.07730.83650.10880.12610.0141-0.02090.24120.02510.160415.665320.168222.7322
40.31-0.2441-0.11550.2610.00750.91710.15790.1921-0.4562-0.1207-0.0199-0.13660.33510.47410.05030.40450.037-0.04160.3091-0.03660.3678.87637.126425.0864
50.79990.0207-0.17560.1484-0.07161.17080.0632-0.0420.20340.2791-0.1334-0.1947-0.4825-0.2779-0.10.1799-0.0578-0.02340.28910.07310.20293.721418.727721.9006
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 47 )A15 - 47
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 60 )A48 - 60
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 107 )A84 - 107
4X-RAY DIFFRACTION4chain 'A' and (resid 135 through 151 )A135 - 151
5X-RAY DIFFRACTION5chain 'A' and (resid 152 through 180 )A152 - 180

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