+Open data
-Basic information
Entry | Database: PDB / ID: 2w4b | ||||||
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Title | Epstein-Barr virus alkaline nuclease D203S mutant | ||||||
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 / symbiont-mediated suppression of host gene expression / host cell nucleus / DNA binding / RNA binding Similarity search - Function | ||||||
Biological species | HUMAN HERPESVIRUS 4 (Epstein-Barr virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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 | 2w4b.cif.gz | 182.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w4b.ent.gz | 146.6 KB | Display | PDB format |
PDBx/mmJSON format | 2w4b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/2w4b ftp://data.pdbj.org/pub/pdb/validation_reports/w4/2w4b | HTTPS FTP |
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-Related structure data
Related structure data | 2w45SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.551, 0.092, -0.83), Vector: |
-Components
#1: Protein | Mass: 52693.773 Da / Num. of mol.: 2 / Mutation: YES 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 Compound details | ENGINEERED | Sequence details | D203S MUTANT | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 60 % / Description: NONE |
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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: Aug 23, 2007 / 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: 3.5→29.99 Å / Num. obs: 13276 / % possible obs: 86 % / Observed criterion σ(I): 0 / Redundancy: 1.92 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.53 |
Reflection shell | Resolution: 3.5→3.53 Å / Redundancy: 1.87 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.02 / % possible all: 88.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2W45 Resolution: 3.5→31.19 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.837 / SU B: 27.406 / SU ML: 0.429 / Cross valid method: THROUGHOUT / ESU R Free: 0.708 / 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: 46.332 Å2
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Refinement step | Cycle: LAST / Resolution: 3.5→31.19 Å
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Refine LS restraints |
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