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- PDB-1vhi: EPSTEIN BARR VIRUS NUCLEAR ANTIGEN-1 DNA-BINDING DOMAIN, RESIDUES... -

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Basic information

Entry
Database: PDB / ID: 1vhi
TitleEPSTEIN BARR VIRUS NUCLEAR ANTIGEN-1 DNA-BINDING DOMAIN, RESIDUES 470-607
ComponentsEPSTEIN BARR VIRUS NUCLEAR ANTIGEN-1
KeywordsNUCLEAR PROTEIN / DNA-BINDING / ACTIVATOR / ORIGIN-BINDING PROTEIN
Function / homology
Function and homology information


host cell PML body / symbiont-mediated suppression of host antigen processing and presentation / viral latency / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / enzyme-substrate adaptor activity / symbiont-mediated disruption of host cell PML body / regulation of DNA replication / endonuclease activity / DNA-binding transcription factor activity / virus-mediated perturbation of host defense response ...host cell PML body / symbiont-mediated suppression of host antigen processing and presentation / viral latency / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / enzyme-substrate adaptor activity / symbiont-mediated disruption of host cell PML body / regulation of DNA replication / endonuclease activity / DNA-binding transcription factor activity / virus-mediated perturbation of host defense response / positive regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Epstein Barr virus nuclear antigen-1, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding / Epstein Barr virus nuclear antigen-1, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / E2/EBNA1, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Epstein-Barr nuclear antigen 1
Similarity search - Component
Biological speciesHuman herpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.5 Å
AuthorsBochkarev, A. / Barwell, J. / Pfuetzner, R. / Furey, W. / Edwards, A. / Frappier, L.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1995
Title: Crystal structure of the DNA-binding domain of the Epstein-Barr virus origin-binding protein EBNA 1.
Authors: Bochkarev, A. / Barwell, J.A. / Pfuetzner, R.A. / Furey Jr., W. / Edwards, A.M. / Frappier, L.
#1: Journal: J.Biol.Chem. / Year: 1995
Title: Overexpression, Purification, and Crystallization of the DNA Binding and Dimerization Domains of the Epstein-Barr Virus Nuclear Antigen 1
Authors: Barwell, J.A. / Bochkarev, A. / Pfuetzner, R.A. / Tong, H. / Yang, D.S. / Frappier, L. / Edwards, A.M.
History
DepositionOct 5, 1996Processing site: BNL
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EPSTEIN BARR VIRUS NUCLEAR ANTIGEN-1
B: EPSTEIN BARR VIRUS NUCLEAR ANTIGEN-1


Theoretical massNumber of molelcules
Total (without water)30,7272
Polymers30,7272
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-19 kcal/mol
Surface area12310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.990, 69.080, 70.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein EPSTEIN BARR VIRUS NUCLEAR ANTIGEN-1 / EBNA1


Mass: 15363.729 Da / Num. of mol.: 2
Fragment: DNA-BINDING AND DIMERIZATION DOMAIN RESIDUES 470 - 607
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 4 (Epstein-Barr virus)
Genus: Lymphocryptovirus / Strain: GD1 / Gene: E2 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: P03211
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.37 Å3/Da / Density % sol: 40 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: HANGING DROP VAPOR DIFFUSION, 50 MM MES PH 6.0 AND 100 MM NACL. SEE REFERENCE 1 FOR MORE DETAILS., vapor diffusion - hanging drop
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17-8 mg/mlprotein1drop
21 mMHEPES1drop
3500 mM1dropNaCl
410 mMDTT1drop
550 mMMES1reservoir
60-150 mM1reservoirNaCl
710 mMDTT1reservoir

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 7, 1994 / Details: DOUBLE MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→35 Å / Num. obs: 10110 / % possible obs: 95.9 % / Observed criterion σ(I): 1 / Redundancy: 8.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.7
Reflection shellResolution: 2.5→2.54 Å / Mean I/σ(I) obs: 5.5 / % possible all: 91.3
Reflection
*PLUS
Num. measured all: 83324

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3model building
X-PLOR3refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.5→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.179 --
obs0.179 9721 95.5 %
Displacement parametersBiso mean: 14.4 Å2
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2071 0 0 71 2142
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2
X-RAY DIFFRACTIONx_mcangle_it2.5
X-RAY DIFFRACTIONx_scbond_it2.5
X-RAY DIFFRACTIONx_scangle_it3
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARAM19X.PRO
X-RAY DIFFRACTION2

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