[English] 日本語
Yorodumi
- PDB-7xy0: HapR Double mutant Y76F, F171C -

+
Open data


ID or keywords:

Loading...

-
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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more