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- PDB-7xy0: HapR Double mutant Y76F, F171C -

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Basic information

Entry
Database: PDB / ID: 7xy0
TitleHapR Double mutant Y76F, 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: 2.43 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

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin/protease regulatory protein
B: Hemagglutinin/protease regulatory protein


Theoretical massNumber of molelcules
Total (without water)47,3252
Polymers47,3252
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-17 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.699, 85.677, 109.838
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: 23662.361 Da / Num. of mol.: 2 / Mutation: Y76F, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 12% PEG 8000, 100 mM Tris pH 8.5, 200 mM MgCl2

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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 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.43→26.11 Å / Num. obs: 30704 / % possible obs: 98 % / Redundancy: 12.4 % / CC1/2: 0.99 / Net I/σ(I): 10.1
Reflection shellResolution: 2.43→2.52 Å / Rmerge(I) obs: 0.952 / Num. unique obs: 1584

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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: 2.43→25.338 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2806 3004 10.02 %
Rwork0.2273 26966 -
obs0.2327 29970 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 180.86 Å2 / Biso mean: 53.9375 Å2 / Biso min: 15.55 Å2
Refinement stepCycle: final / Resolution: 2.43→25.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3221 0 0 70 3291
Biso mean---36.77 -
Num. residues----394
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.4301-2.46990.38951440.33491266
2.4699-2.51250.35111410.32381309
2.5125-2.55810.38111450.30541277
2.5581-2.60730.41331490.30471292
2.6073-2.66040.33791430.31451280
2.6604-2.71820.39841420.30811270
2.7182-2.78140.35531410.27821278
2.7814-2.85090.28891500.25951301
2.8509-2.92780.36051460.27361278
2.9278-3.01380.35631410.27311258
3.0138-3.1110.32571510.24881333
3.111-3.22190.3091350.24271262
3.2219-3.35070.29371420.2461290
3.3507-3.50280.25121440.22131263
3.5028-3.68690.2921460.21961299
3.6869-3.91710.23261420.2111285
3.9171-4.21830.22391430.18811280
4.2183-4.64050.23521410.16761273
4.6405-5.30660.24511390.18091297
5.3066-6.66560.24331350.21331283
6.6656-25.330.20941440.16781292
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)
12.10922.301-0.08214.84961.66623.3363-0.6133-0.9075-0.06461.00870.9125-1.11070.86481.4037-0.28420.68560.1149-0.14610.36730.06620.3395-3.8353-7.174-1.2985
22.2149-1.92273.75273.2199-2.04277.2041-0.72280.12871.40450.2311.283.4473-1.831-1.0901-1.29570.79590.19060.39890.71670.20981.3351-13.527626.2598-36.9841
35.60170.3039-0.87418.6402-4.21558.14930.1831-0.4334-0.0271-0.42330.17860.28690.2002-0.0858-0.42890.234-0.04570.02110.4545-0.01470.1331-8.128316.7822-33.5414
41.8424-0.2714-2.15323.6414-1.91733.7466-0.0324-0.0203-0.05970.1346-0.1806-0.131-0.19170.73720.17190.2811-0.1112-0.03530.2771-0.0490.1831-0.978816.674-28.9558
55.19670.40790.7452.4667-2.47725.6789-0.0450.23370.26660.4436-0.18530.06460.18710.40510.15960.5316-0.02570.02610.2586-0.05550.22-7.229312.1882-12.8633
63.00531.5342-2.0784.60874.1059.30620.55550.0102-0.15630.1523-0.5835-1.1619-0.17430.88510.24240.5784-0.0233-0.01080.45750.19020.5494.59128.049-9.5115
72.00963.8816-0.51935.48370.87221.95740.0299-2.3316-0.53622.1576-1.3286-0.8046-1.17410.342-0.2441.18120.2091-0.32180.8613-0.02350.43772.11224.94326.3092
82.5203-1.7871-0.63274.761-2.94995.04430.08610.0335-0.00980.20280.02380.243-0.5973-0.2427-0.05120.51970.0270.05280.2009-0.0540.2446-13.17247.9055-6.5491
92.49921.4340.69295.67880.64973.2428-0.66121.2577-0.3903-0.48550.9791-0.6471-0.5990.8168-0.69880.640.2237-0.08530.6955-0.25270.7161-9.6677-23.8907-37.6256
104.5541.4312.28694.1953.14535.8287-1.14020.80120.0016-1.4871.00330.1866-1.61451.12560.26930.8025-0.1716-0.1530.53110.01570.1725-16.1847-15.8292-34.8973
112.45130.9360.63242.75471.66532.26930.1825-0.1394-0.1387-1.0490.06150.71081.328-1.39480.24850.6849-0.0292-0.13260.2915-0.08160.2611-20.9775-13.4317-20.4672
125.9229-0.1823-3.86113.1831-1.08519.88490.3068-0.3651-0.34940.198-0.2034-0.110.1760.58450.11740.48460.0082-0.02680.19020.01150.2359-11.6531-14.4572-3.5304
132.8986-0.619-0.64789.2016-3.00215.4874-0.22220.1618-0.124-0.5870.07810.1429-0.4796-0.18660.13870.58120.0602-0.12750.31780.02390.1535-12.7961-9.3214-19.7428
144.17810.2420.56974.40651.51882.1554-0.37750.79651.3457-1.1980.51011.808-0.0888-0.0574-0.41020.95590.1425-0.28610.69250.11150.5281-22.33930.2187-21.0884
155.41240.90531.37047.2541.37475.29640.96940.192-0.12670.2941-0.32590.6413-0.1438-0.5286-0.27070.38790.10070.07390.36850.01630.3712-24.9432-7.4201-2.1165
163.52330.3931-2.44555.096-3.11788.16790.2502-0.19160.2561-0.01550.01970.044-0.28070.301-0.27050.44150.0708-0.02640.19920.02720.2298-13.256-2.9449-4.0717
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 182 through 202 )B182 - 202
2X-RAY DIFFRACTION2chain 'A' and (resid 5 through 14 )A5 - 14
3X-RAY DIFFRACTION3chain 'A' and (resid 15 through 47 )A15 - 47
4X-RAY DIFFRACTION4chain 'A' and (resid 48 through 83 )A48 - 83
5X-RAY DIFFRACTION5chain 'A' and (resid 84 through 126 )A84 - 126
6X-RAY DIFFRACTION6chain 'A' and (resid 127 through 150 )A127 - 150
7X-RAY DIFFRACTION7chain 'A' and (resid 151 through 159 )A151 - 159
8X-RAY DIFFRACTION8chain 'A' and (resid 160 through 200 )A160 - 200
9X-RAY DIFFRACTION9chain 'B' and (resid 5 through 14 )B5 - 14
10X-RAY DIFFRACTION10chain 'B' and (resid 15 through 60 )B15 - 60
11X-RAY DIFFRACTION11chain 'B' and (resid 61 through 83 )B61 - 83
12X-RAY DIFFRACTION12chain 'B' and (resid 84 through 107 )B84 - 107
13X-RAY DIFFRACTION13chain 'B' and (resid 108 through 119 )B108 - 119
14X-RAY DIFFRACTION14chain 'B' and (resid 120 through 134 )B120 - 134
15X-RAY DIFFRACTION15chain 'B' and (resid 135 through 150 )B135 - 150
16X-RAY DIFFRACTION16chain 'B' and (resid 151 through 181 )B151 - 181

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