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- PDB-8pw2: Protein p6 from bacteriophage phi29, C-terminal delta31 truncated... -

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Basic information

Entry
Database: PDB / ID: 8pw2
TitleProtein p6 from bacteriophage phi29, C-terminal delta31 truncated version
ComponentsHistone-like protein p6
KeywordsDNA BINDING PROTEIN / histone-like / bacillus subtillis phage / phi29 / nucleocomplex / p6 / DNA superhelix
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: 1.59 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


Theoretical massNumber of molelcules
Total (without water)8,2961
Polymers8,2961
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.257, 59.257, 41.668
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

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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: 8295.601 Da / Num. of mol.: 1
Mutation: last 31 residues are not included in the construct
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.: 27 / 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: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 100 mM Bis Tris Propane pH 7.0 and 1.3 M di-Ammonium Tartrate

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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: Jun 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.59→41.67 Å / Num. obs: 11565 / % possible obs: 99.3 % / Redundancy: 19.5 % / Biso Wilson estimate: 29.79 Å2 / CC1/2: 1 / Net I/σ(I): 37.3
Reflection shellResolution: 1.59→1.62 Å / Rmerge(I) obs: 1.026 / Num. unique obs: 550 / CC1/2: 0.94

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Processing

Software
NameVersionClassification
MxCuBE1.20_4459data collection
PHENIX1.20_4459refinement
MxCuBE1.20_4459data collection
MxCuBE1.20_4459data collection
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→32.35 Å / SU ML: 0.1996 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 31.6069
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2163 569 4.92 %
Rwork0.2126 10986 -
obs0.2128 11555 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.59 Å2
Refinement stepCycle: LAST / Resolution: 1.59→32.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms474 0 0 27 501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093508
X-RAY DIFFRACTIONf_angle_d1.0759697
X-RAY DIFFRACTIONf_chiral_restr0.066485
X-RAY DIFFRACTIONf_plane_restr0.010190
X-RAY DIFFRACTIONf_dihedral_angle_d4.960671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.750.31711510.29032657X-RAY DIFFRACTION97.98
1.75-20.28111530.23022706X-RAY DIFFRACTION98.82
2-2.520.25821150.24972758X-RAY DIFFRACTION99.34
2.52-32.350.19061500.19412865X-RAY DIFFRACTION99.8
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)
12.607553503051.76834106364-0.1479168638034.632806034990.4389464223061.034450981120.0506328774630.06969776830940.2016525740760.2585212614090.174987457927-0.45426690941-0.1834417666490.0837778245729-0.1721969574810.2816339013490.0067957768980.004086361443780.254499285215-0.04106963426520.27562989424535.1348957307-5.37873426866-2.21255148682
24.047452314882.30001634746-0.5939080452744.90123286165-0.4087959631773.24369020787-0.02106381603460.1666430912720.5965229717060.2598562833850.1130363580940.531891946819-0.299745385352-0.227633414858-0.08402658868010.2595958356890.03164826045350.01127489593970.2507673201050.02355060057110.27736963216523.5070923977-11.8441891746-1.77752144364
35.813392095571.65582562851-0.810070131990.954377974269-1.404545393883.07110115229-0.114061609895-0.06185597448450.04964536520220.5910902501030.03494630296210.243470496944-0.05532008750320.101458427841-0.2036646935590.320211541264-0.01641389145930.01722485927280.297193540833-0.006531089244020.21344403482928.5406753923-11.1732609944-3.59466488983
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 8 through 29 )8 - 291 - 22
22chain 'A' and (resid 30 through 51 )30 - 5123 - 44
33chain 'A' and (resid 52 through 67 )52 - 6745 - 60

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