[English] 日本語
Yorodumi
- PDB-8pw4: Protein p6 from bacteriophage phi29, C-terminal delta20 truncated... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pw4
TitleProtein p6 from bacteriophage phi29, C-terminal delta20 truncated version
ComponentsHistone-like protein p6
KeywordsDNA BINDING PROTEIN / histone-like / bacillus subtillis phage / phi29 / nucleocomplex / p6 / DNA superhelix / protein oligomer
Function / homology
Function and homology information


regulation of viral transcription / viral DNA genome replication / chromosome condensation / DNA-binding transcription repressor activity / transcription repressor complex / DNA replication / DNA-templated transcription / DNA binding
Similarity search - Function
Histone-like protein p6 / Histone-like Protein p6
Similarity search - Domain/homology
Histone-like protein p6
Similarity search - Component
Biological speciesSalasvirus phi29
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAlcorlo Pages, M. / Hermoso Dominguez, J.
Funding support Spain, Switzerland, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-115331GB-I00 Spain
Swiss National Science FoundationCRSII5_198737/1 Switzerland
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Flexible structural arrangement and DNA-binding properties of protein p6 from Bacillus subtillis phage phi 29.
Authors: Alcorlo, M. / Luque-Ortega, J.R. / Gago, F. / Ortega, A. / Castellanos, M. / Chacon, P. / de Vega, M. / Blanco, L. / Hermoso, J.M. / Serrano, M. / Rivas, G. / Hermoso, J.A.
History
DepositionJul 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone-like protein p6
B: Histone-like protein p6


Theoretical massNumber of molelcules
Total (without water)19,1402
Polymers19,1402
Non-polymers00
Water23413
1
A: Histone-like protein p6


Theoretical massNumber of molelcules
Total (without water)9,5701
Polymers9,5701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone-like protein p6


Theoretical massNumber of molelcules
Total (without water)9,5701
Polymers9,5701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.185, 44.185, 206.735
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-101-

HOH

-
Components

#1: Protein Histone-like protein p6 / Double-stranded DNA-binding protein p6 / Gene product 6 / gp6 / Nucleoid-associated protein p6 / Protein p6


Mass: 9570.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salasvirus phi29 / Production host: Escherichia coli (E. coli) / References: UniProt: P03685
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.04 Å3/Da / Density % sol: 59.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 8000; 20% v/v ethylene glycol; 0.02 M 1,6-hexanediol; 0.02 M 1-butanol; 0.02 M (RS)-1,2-propanediol; 0.02 M 2-propanol; 0.02 M 1,4-butanediol; 0.02 M 1,3-propanediol and 0.1 M MES/imidazole pH 6.5.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→41.35 Å / Num. obs: 11226 / % possible obs: 100 % / Redundancy: 18.8 % / Biso Wilson estimate: 52.95 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.086 / Net I/σ(I): 24
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 1.035 / Num. unique obs: 1059 / CC1/2: 0.89

-
Processing

Software
NameVersionClassification
MxCuBE1.20_4459data collection
PHENIX1.20_4459refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→14.7 Å / SU ML: 0.3599 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.7901
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2748 599 5.39 %
Rwork0.2407 10511 -
obs0.2425 11110 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.89 Å2
Refinement stepCycle: LAST / Resolution: 2.3→14.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1334 0 0 13 1347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00331359
X-RAY DIFFRACTIONf_angle_d0.84341837
X-RAY DIFFRACTIONf_chiral_restr0.0453215
X-RAY DIFFRACTIONf_plane_restr0.0052236
X-RAY DIFFRACTIONf_dihedral_angle_d10.084180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.530.3061360.33462557X-RAY DIFFRACTION100
2.53-2.890.36261590.3042561X-RAY DIFFRACTION99.96
2.89-3.640.34051570.28992618X-RAY DIFFRACTION100
3.64-14.70.21981470.19222775X-RAY DIFFRACTION100
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)
11.45279118251-0.842178309948-1.589143962711.99750935268-0.4233816787462.638085511290.1280936605870.619002463223-0.0610075635189-0.513771788031-0.168602461328-0.2318263991850.939625981771-0.4198619814640.09332459281220.551557698422-0.04984609053030.04312896910070.633215681848-0.1010932194190.3977234746371.64317904829-8.8890941941513.013334811
23.821455585490.0241397084517-0.1110499374743.099061885920.836802332215.43171504604-0.0810161923664-0.1083873026581.125416132690.04492077254550.655838355558-0.307487264038-0.6425219887070.255537549804-0.4138048581520.372239158851-0.06045364811770.0307919130920.4301773408230.005440669303010.416142494908-7.111582257445.7241035396635.2662904932
32.08557408107-1.332854364980.1018300615513.17565992911-0.6828623677172.323449158890.07956551874640.213505989398-0.5900721597920.243011276763-0.2666091086740.4291848776290.696950553891-0.5382075543850.2706531473560.577297139846-0.1316808813230.06190624793050.592587295152-0.09375180579610.645633746509-3.63552602576-11.641115844523.4112083625
40.280947828405-1.5264201869-1.390589458523.529799954283.905178370063.431334166120.4272485609570.1352478733320.324870751588-0.9493225136960.0279361175793-0.556009459989-0.6090987795880.110760127337-0.5702309467380.780786102995-0.01872799866450.238741992760.799147975944-0.05711708179020.6317161530069.0991679156-14.26402660993.53388120409
51.78714589554-0.894450552302-2.40786892912.813943227980.8833776116123.654169319220.2051004579860.4388294514450.0592363670177-0.231287209276-0.118790667932-0.3785819193510.359203756293-0.8918721867840.04700375455490.372658660642-0.04842292451730.02003632389390.578799179393-0.04922304876290.49321760189611.94986039634.7542741688716.9894429064
66.749948953880.4565141460550.128280686712.988457230871.961668814753.68749472370.2108720985550.108137669160.14668060920.1722538002160.285874687766-0.580727906541-0.2053000732840.803839260188-0.3617406621340.429132609628-0.1042468820970.01209858359780.4689955470220.02358804986960.46423844707914.137096518.7453599982329.600502911
70.882478581649-0.630951231163-0.9112829510222.698404584521.8940863192.251501649320.2289108853680.5250098812040.0997190322115-0.8583548442210.253952470851-0.307190265077-0.67605659466-0.270700872771-0.2862983985470.579180638312-0.1774002111250.1256024928870.680554569305-0.01569321417160.47101666734913.39248280143.922870960498.9161901376
80.5657627540310.345611482224-1.879726627312.7427103210.7218854200697.689285793220.394191548912-0.274003403917-0.04427035212061.309674218340.699450896653-1.253466033530.5208167632261.97567605507-0.8973118663231.59011756158-0.458710277960.07269386857421.32282949419-0.6826621449751.3775890529830.55208301996.567386268431.40914257067
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 21 )AA1 - 211 - 21
22chain 'A' and (resid 22 through 29 )AA22 - 2922 - 29
33chain 'A' and (resid 30 through 56 )AA30 - 5630 - 56
44chain 'A' and (resid 57 through 83 )AA57 - 8357 - 83
55chain 'B' and (resid 1 through 21 )BB1 - 211 - 21
66chain 'B' and (resid 22 through 56 )BB22 - 5622 - 56
77chain 'B' and (resid 57 through 78 )BB57 - 7857 - 78
88chain 'B' and (resid 79 through 83 )BB79 - 8379 - 83

+
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