+Open data
-Basic information
Entry | Database: PDB / ID: 2w45 | ||||||
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Title | Epstein-Barr virus alkaline nuclease | ||||||
Components | ALKALINE EXONUCLEASE | ||||||
Keywords | HYDROLASE / EXONUCLEASE / ENDONUCLEASE / GAMMA-HERPESVIRUS / EBV / BGLF5 / DNASE / NUCLEASE / HERPESVIRUS / EPSTEIN-BARR VIRUS | ||||||
Function / homology | Function and homology information exonuclease activity / symbiont-mediated degradation of host mRNA / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / host cell nucleus / DNA binding / RNA binding Similarity search - Function | ||||||
Biological species | HUMAN HERPESVIRUS 4 (Epstein-Barr virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3 Å | ||||||
Authors | Buisson, M. / Geoui, T. / Flot, D. / Tarbouriech, N. / Burmeister, W.P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: A Bridge Crosses the Active Site Canyon of the Epstein-Barr Virus Nuclease with DNase and Rnase Activity. Authors: Buisson, M. / Geoui, T. / Flot, D. / Tarbouriech, N. / Ressing, M.E. / Wiertz, E.J. / Burmeister, W.P. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w45.cif.gz | 180 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w45.ent.gz | 145.1 KB | Display | PDB format |
PDBx/mmJSON format | 2w45.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w45_validation.pdf.gz | 446.6 KB | Display | wwPDB validaton report |
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Full document | 2w45_full_validation.pdf.gz | 499.8 KB | Display | |
Data in XML | 2w45_validation.xml.gz | 38.3 KB | Display | |
Data in CIF | 2w45_validation.cif.gz | 51.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/2w45 ftp://data.pdbj.org/pub/pdb/validation_reports/w4/2w45 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.551, 0.092, -0.83), Vector: |
-Components
#1: Protein | Mass: 52721.781 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN HERPESVIRUS 4 (Epstein-Barr virus) Strain: B95-8 / Plasmid: PFASTBAC HTB / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) References: UniProt: P03217, Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 60 % Description: PHASING USED 6 INCOMPLETE DATASETS COLLECTED AT DIFFERENT WAVELENGTH WITH SLIGHTLY DIFFERENT HA PARAMETERS. |
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Crystal grow | pH: 7.5 Details: PROTEIN AT 4.5 MG/ML IN 250 MM NACL, 20MM TRIS PH 7.5, RESERVOIR:10 MM DTT, 10 MM MGCL2, 0.1M HEPES PH 7.0, 1.5% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 17, 2006 / Details: MIRRORS |
Radiation | Monochromator: CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 3→71.8 Å / Num. obs: 24158 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 5.77 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 3.59 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.58 / % possible all: 96.48 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS Starting model: NONE Resolution: 3→71.43 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.828 / SU B: 16.159 / SU ML: 0.308 / Cross valid method: THROUGHOUT / ESU R Free: 0.484 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.778 Å2
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Refinement step | Cycle: LAST / Resolution: 3→71.43 Å
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