[English] 日本語
Yorodumi
- PDB-7e90: Crystal structure of the receiver domain (D51E) of the response r... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7.0E+90
TitleCrystal structure of the receiver domain (D51E) of the response regulator VbrR from Vibrio parahaemolyticus
ComponentsDNA-binding response regulator
KeywordsTRANSCRIPTION / transcriptional regulation / receiver domain / response regulator / VbrR / Vibrio parahaemolyticus
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA-binding response regulator
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsCho, S.Y. / Yoon, S.I.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Structural analysis of the activation and DNA interactions of the response regulator VbrR from Vibrio parahaemolyticus.
Authors: Cho, S.Y. / Yoon, S.I.
History
DepositionMar 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-binding response regulator
B: DNA-binding response regulator


Theoretical massNumber of molelcules
Total (without water)27,9522
Polymers27,9522
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.128, 74.128, 108.438
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSPROPRO(chain 'A' and ((resid 2 and (name N or name...AA2 - 648 - 70
12TRPTRPARGARG(chain 'A' and ((resid 2 and (name N or name...AA66 - 11672 - 122
23LYSLYSPROPRO(chain 'B' and (resid 2 through 27 or (resid 28...BB2 - 648 - 70
24TRPTRPARGARG(chain 'B' and (resid 2 through 27 or (resid 28...BB66 - 11672 - 122

-
Components

#1: Protein DNA-binding response regulator


Mass: 13976.006 Da / Num. of mol.: 2 / Fragment: receiver domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: C1S91_03975 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2R9VV79
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 400, Tris, lithium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 14862 / % possible obs: 99.7 % / Redundancy: 5 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 21.4
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.546 / Num. unique obs: 708 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZWM

2zwm


Resolution: 2.25→30 Å / SU ML: 0.211 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.011
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.273 722 4.89 %
Rwork0.233 14056 -
obs0.2346 14056 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.1 Å2
Refinement stepCycle: LAST / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 0 34 1820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411814
X-RAY DIFFRACTIONf_angle_d0.8042471
X-RAY DIFFRACTIONf_chiral_restr0.0516299
X-RAY DIFFRACTIONf_plane_restr0.0053318
X-RAY DIFFRACTIONf_dihedral_angle_d20.3191109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.430.25991470.25542697X-RAY DIFFRACTION98.58
2.43-2.670.29661460.27332759X-RAY DIFFRACTION99.42
2.67-3.060.28781230.26522803X-RAY DIFFRACTION99.63
3.06-3.850.3081250.22792849X-RAY DIFFRACTION99.66
3.85-300.25291810.21232948X-RAY DIFFRACTION99.4
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)
14.07834324049-0.331723965521-0.9630880225263.447547237111.104858953655.23531885846-0.1554056916080.5155659657780.0788398389477-0.133601489971-0.1201989986150.1816637997790.0451788970316-0.3051587546140.2288325325020.346960192643-0.00908947286104-0.01500143143980.3557023298160.03167896513020.248675065707-15.2304985253-25.18245051149.10054858021
27.10288605650.908714406114-1.007577177912.67963346834-1.477708156054.53722969351-0.341940797430.9405121287721.11353371183-0.6948866406670.01578979492460.171551023693-0.667495710832-0.01499897868510.1494181749110.5299500561760.00107058747808-0.1274279456390.3232899202570.09051161633620.483751538522-11.3666345442-14.381523486110.4373118643
32.68245226529-0.388087850413-2.130995573322.6115011607-0.2694921966297.142140530780.3343298362430.07540644340320.740578998892-0.437424910292-0.21115483260.0328385401111-1.195626839570.6317114981-0.08357508886420.611843723309-0.166752061073-0.01740360705630.4789362889750.0298518261290.40880270898-5.69811685967-14.663355224216.7496068535
44.141870362330.6904914697961.140557655792.89216423481.225342017965.95853072821-0.2100192006830.07910071346970.242822919918-0.004453088845010.01760012717740.134069331787-0.323045529040.06363788905670.1804660000720.2895208137160.008975713542130.03708584682370.1949314578870.0228471781170.189285762424-8.86913084422-24.350768705423.2299601862
54.04712927236-0.197605063404-0.8283374184351.10999690646-0.9960887096294.94764443902-0.233452441394-0.2549886135180.05715416905260.1506293808810.145932904098-0.4305376344830.352880422107-0.0366374054650.1005188693050.3378632415210.0629053533461-0.01020702395560.339312123752-0.1053761010630.250640955632-8.43006397952-22.208589198346.9902567046
65.863786062493.29937443294-2.336039627825.3296562908-1.614616800837.191253949540.727523646552-0.6153498047270.9504523146180.638076065983-0.007416143459230.632985255389-1.00851046723-0.196952857252-0.4175857928170.4892447083620.01371412285450.09648893821130.39480113617-0.1750387532190.392737312895-11.6583753905-17.067790470247.1674129526
77.746205847542.96005910846-1.283495762795.36812874668-0.6695025251356.90274033058-0.20498065586-0.6948874078850.6003655810380.8101352067230.0929031044614-0.08893528210030.361679231401-1.64875447174-0.1122722292450.518877044082-0.04660176255530.0391471410760.652799058249-0.0677514993380.323756061426-22.4496505551-23.413238447947.9528945708
83.282533781630.05961748339580.1817816973623.471534706310.8655992011475.30724643108-0.0436112543124-0.36781768626-0.1700940182410.510250121234-0.0853932283031-0.05704969244770.903418575031-0.4106043260160.1896750826910.428240507481-0.0541721709479-0.01255957357190.460086946247-0.0494255446290.241608058804-17.2410436449-28.790592184542.1222084213
95.34420153328-0.9199150912010.9397194130817.170965326670.6452880998537.404680393820.340218966132-0.504539422659-0.9022679529671.22875497309-0.525050498920.9066576459740.494301787781-1.749294569250.2900609678960.345389024663-0.150643927940.02354324229640.823122116011-0.09322641262860.502748495317-26.233759098-27.339783685438.9534770576
103.345873636480.6185653906680.864650960914.138402515471.216707295225.24725277206-0.3447903969520.219498483569-0.3988867872180.1722006159830.1913108248840.1820552627950.549405096012-0.6748491912170.1439857033910.407932589176-0.03124504693970.0166506380920.3558988962947.12685519587E-50.235046032001-14.6259799997-28.912527516133.3869827142
112.27514686953-0.2206075624531.463955004915.245735873841.064676910658.29938965618-0.008598006479050.008058029999931.11270245588-0.207402238539-0.231659353280.256169770817-0.628994948847-0.1710344597980.104316105980.5180917814770.05841449154060.0406101232660.2485985201050.02016019496080.399994546037-7.50665504537-17.893102396734.1614766488
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 50 )
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 78 )
4X-RAY DIFFRACTION4chain 'A' and (resid 79 through 116 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 24 )
6X-RAY DIFFRACTION6chain 'B' and (resid 25 through 32 )
7X-RAY DIFFRACTION7chain 'B' and (resid 33 through 44 )
8X-RAY DIFFRACTION8chain 'B' and (resid 45 through 58 )
9X-RAY DIFFRACTION9chain 'B' and (resid 59 through 69 )
10X-RAY DIFFRACTION10chain 'B' and (resid 70 through 103 )
11X-RAY DIFFRACTION11chain 'B' and (resid 104 through 116 )

+
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