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- PDB-8pw4: Protein p6 from bacteriophage phi29, C-terminal delta20 truncated... -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 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.

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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

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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

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