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- PDB-6bus: Extended E2 DNA-binding domain of the Bovine Papillomavirus-1 -

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Basic information

Entry
Database: PDB / ID: 6bus
TitleExtended E2 DNA-binding domain of the Bovine Papillomavirus-1
ComponentsRegulatory protein E2
KeywordsDNA BINDING PROTEIN / Open reading frame / E2 / BPV-1
Function / homology
Function and homology information


viral DNA genome replication / regulation of DNA replication / DNA replication / DNA-binding transcription factor activity / nucleotide binding / DNA-templated transcription / host cell nucleus / DNA binding
Similarity search - Function
Papillomavirus E2, C-terminal / Papillomavirus E2, N-terminal / Regulatory protein E2 / E2 regulatory, transactivation domain / E2 regulatory, transactivation domain, subdomain 1 / E2 regulatory, transactivation domain, subdomain 2 / E2 (early) protein, N terminal / E2 (early) protein, C terminal / E2/EBNA1, C-terminal / RRM (RNA recognition motif) domain ...Papillomavirus E2, C-terminal / Papillomavirus E2, N-terminal / Regulatory protein E2 / E2 regulatory, transactivation domain / E2 regulatory, transactivation domain, subdomain 1 / E2 regulatory, transactivation domain, subdomain 2 / E2 (early) protein, N terminal / E2 (early) protein, C terminal / E2/EBNA1, C-terminal / RRM (RNA recognition motif) domain / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Regulatory protein E2
Similarity search - Component
Biological speciesBovine papillomavirus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLeroy, L.M.D. / Barbosa, J.A.R.G. / Polikarpov, I. / Pinheiro, C.B.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior Brazil
CitationJournal: Proteins / Year: 2020
Title: The structure of the extended E2 DNA-binding domain of the bovine papillomavirus-1.
Authors: Leroy, L. / Barbosa, J.A.R.G. / de Prat-Gay, G. / Polikarpov, I. / Pinheiro, C.B.
History
DepositionDec 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.3Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: Regulatory protein E2
2: Regulatory protein E2
3: Regulatory protein E2
4: Regulatory protein E2


Theoretical massNumber of molelcules
Total (without water)46,3094
Polymers46,3094
Non-polymers00
Water3,549197
1
1: Regulatory protein E2
2: Regulatory protein E2


Theoretical massNumber of molelcules
Total (without water)23,1542
Polymers23,1542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-8 kcal/mol
Surface area10300 Å2
MethodPISA
2
3: Regulatory protein E2
4: Regulatory protein E2


Theoretical massNumber of molelcules
Total (without water)23,1542
Polymers23,1542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-10 kcal/mol
Surface area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.203, 55.203, 203.091
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Regulatory protein E2


Mass: 11577.162 Da / Num. of mol.: 4 / Fragment: UNP Residues 310-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine papillomavirus type 1 / Gene: E2 / Production host: Escherichia coli (E. coli) / References: UniProt: P03122
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 1.93 Å3/Da / Density % sol: 36.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: sodium citrate, PEG 4000 and ammonium acetate / PH range: 4.6-5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.39 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.39 Å / Relative weight: 1
ReflectionResolution: 1.9→67.8 Å / Num. obs: 29354 / % possible obs: 99.8 % / Redundancy: 5.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.045 / Net I/σ(I): 10.2
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 1816 / CC1/2: 0.543 / Rpim(I) all: 0.419 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BOP

2bop


Resolution: 1.9→67.79 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.903 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.169
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2605 1457 5 %RANDOM
Rwork0.2138 ---
obs0.2161 29287 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 91.97 Å2 / Biso mean: 28.8264 Å2 / Biso min: 8.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0.14 Å2-0 Å2
2---0.28 Å20 Å2
3---0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.9→67.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2921 0 0 197 3118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192994
X-RAY DIFFRACTIONr_bond_other_d00.022692
X-RAY DIFFRACTIONr_angle_refined_deg1.7631.9224040
X-RAY DIFFRACTIONr_angle_other_deg3.74836237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9895367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.53922.808146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.39315486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3681524
X-RAY DIFFRACTIONr_chiral_restr0.1080.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213376
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02680
X-RAY DIFFRACTIONr_mcbond_it2.5092.7761480
X-RAY DIFFRACTIONr_mcbond_other2.5082.7761479
X-RAY DIFFRACTIONr_mcangle_it3.8984.1471843
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 113 -
Rwork0.345 1997 -
all-2110 -
obs--99.39 %

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