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- PDB-6lqn: EBV tegument protein BBRF2 -

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Basic information

Entry
Database: PDB / ID: 6lqn
TitleEBV tegument protein BBRF2
ComponentsCytoplasmic envelopment protein 1
KeywordsVIRAL PROTEIN / Epstein-Barr virus (EBV) / Human herpesvirus 4 (HHV-4) / tegument protein BBEF2 / Cytoplasmic envelopment protein 1 (CEP1_EBVB9)
Function / homologyHerpesvirus UL7-like / Herpesvirus UL7 like / viral tegument / host cell Golgi apparatus / NITRATE ION / Cytoplasmic envelopment protein 1 / Cytoplasmic envelopment protein 1
Function and homology information
Biological speciesHuman gammaherpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.60002201523 Å
AuthorsHe, H.P. / Luo, M. / Cao, Y.L. / Gao, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2020
Title: Structure of Epstein-Barr virus tegument protein complex BBRF2-BSRF1 reveals its potential role in viral envelopment.
Authors: He, H.P. / Luo, M. / Cao, Y.L. / Lin, Y.X. / Zhang, H. / Zhang, X. / Ou, J.Y. / Yu, B. / Chen, X. / Xu, M. / Feng, L. / Zeng, M.S. / Zeng, Y.X. / Gao, S.
History
DepositionJan 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytoplasmic envelopment protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9654
Polymers30,7111
Non-polymers2543
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-13 kcal/mol
Surface area13100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.320, 61.570, 58.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Components on special symmetry positions
IDModelComponents
11A-301-

SO4

21A-542-

HOH

31A-573-

HOH

41A-642-

HOH

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Components

#1: Protein Cytoplasmic envelopment protein 1


Mass: 30711.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human gammaherpesvirus 4 (Epstein-Barr virus)
Strain: GD1 / Gene: BBRF2 / Production host: Escherichia coli (E. coli) / References: UniProt: K9US56, UniProt: Q3KSR8*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.3 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.09 M NPS (0.03 M NaNO3, 0.03 M Na2HPO4, 0.03 M (NH4)2SO4); 0.1 M MES/imidazole pH 6.5; 37.5% precipitants (12.5% PEG1000,12.5% PEG 3350,12.5% MPD)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.6→47.15 Å / Num. obs: 66862 / % possible obs: 99.2 % / Redundancy: 3.41 % / Biso Wilson estimate: 15.3432910578 Å2 / Rrim(I) all: 0.085 / Net I/σ(I): 13.39
Reflection shellResolution: 1.6→1.69 Å / Num. unique obs: 10656 / Rrim(I) all: 0.674

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
REFMACCCP4-7.0refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.60002201523→36.66 Å / SU ML: 0.148203960753 / Cross valid method: NONE / σ(F): 1.00811075143 / Phase error: 18.0415438908
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER F_MINUS AND F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.188803534941 3772 5.65610520476 %
Rwork0.16553383033 62917 -
obs0.166858938464 66689 99.4141498465 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.9450353465 Å2
Refinement stepCycle: LAST / Resolution: 1.60002201523→36.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2081 0 14 278 2373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009468494075052216
X-RAY DIFFRACTIONf_angle_d1.109445299443010
X-RAY DIFFRACTIONf_chiral_restr0.0627574715848346
X-RAY DIFFRACTIONf_plane_restr0.00611488114374384
X-RAY DIFFRACTIONf_dihedral_angle_d19.1989343078864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.60002201523-1.62030.2776224129441380.2422054959832301X-RAY DIFFRACTION97.5209916034
1.6203-1.64160.2416626677881530.2290746472322311X-RAY DIFFRACTION99.9594320487
1.6416-1.66410.2556294136661460.2184332546432371X-RAY DIFFRACTION99.9206034141
1.6641-1.68790.2175054825511350.2127287353042277X-RAY DIFFRACTION100
1.6879-1.7130.2049705472641420.2115108363532383X-RAY DIFFRACTION99.9604117181
1.713-1.73980.2210381979261430.1953512597192344X-RAY DIFFRACTION99.959807074
1.7398-1.76830.2787847275761010.1913701251592384X-RAY DIFFRACTION100
1.7683-1.79880.2714454817761540.1993973316772339X-RAY DIFFRACTION100
1.7988-1.83150.2095336316461540.186742833012317X-RAY DIFFRACTION100
1.8315-1.86680.2240530076571380.1801518922872355X-RAY DIFFRACTION99.959903769
1.8668-1.90490.2330324144151250.1854591267532368X-RAY DIFFRACTION100
1.9049-1.94630.2398008780211420.178172836612321X-RAY DIFFRACTION99.9188640974
1.9463-1.99160.18566351811300.1631070803232355X-RAY DIFFRACTION100
1.9916-2.04140.1705323178991710.1612434955622300X-RAY DIFFRACTION99.9191265669
2.0414-2.09650.1417022953621130.1616120764952363X-RAY DIFFRACTION99.9192897498
2.0965-2.15820.1717417155681560.1503200859032339X-RAY DIFFRACTION99.9199038847
2.1582-2.22790.1683223583431380.1555848442912367X-RAY DIFFRACTION99.9202233746
2.2279-2.30750.1659198169461340.1613385383332327X-RAY DIFFRACTION100
2.3075-2.39990.1979724879681480.1526438073022337X-RAY DIFFRACTION99.7591328784
2.3999-2.50910.1902050327791370.1576030909462327X-RAY DIFFRACTION99.6763754045
2.5091-2.64130.1789167607611500.162456117722349X-RAY DIFFRACTION99.7604790419
2.6413-2.80680.1665439734191320.1654127138342352X-RAY DIFFRACTION99.9195494771
2.8068-3.02340.1630172976681480.1609037592142332X-RAY DIFFRACTION99.7586484312
3.0234-3.32740.1911867326831370.1538102645032315X-RAY DIFFRACTION99.4726166329
3.3274-3.80850.1594349048441450.1424785730682326X-RAY DIFFRACTION99.6370967742
3.8085-4.79660.1790891242761410.1348847373022315X-RAY DIFFRACTION98.4763432237
4.7966-36.660.2063030247851210.1901462174292142X-RAY DIFFRACTION90.9565916399
Refinement TLS params.Method: refined / Origin x: 18.89684623 Å / Origin y: 19.3481600104 Å / Origin z: 17.2474090106 Å
111213212223313233
T0.132963511735 Å2-0.00143386347575 Å2-0.010582582773 Å2-0.0774103315422 Å2-0.0081055987395 Å2--0.10143527058 Å2
L2.02241787566 °20.281677746029 °2-0.0975264593315 °2-0.351369352332 °20.089672711478 °2--0.773028605302 °2
S-0.00695185636421 Å °0.183491526179 Å °-0.0449494082969 Å °-0.0424219200612 Å °0.010138868318 Å °0.032248550063 Å °0.00847173307209 Å °-0.0373015230495 Å °-0.0123832467889 Å °
Refinement TLS groupSelection details: all

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