+Open data
-Basic information
Entry | Database: PDB / ID: 1o6e | ||||||
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Title | Epstein-Barr virus protease | ||||||
Components | CAPSID PROTEIN P40 | ||||||
Keywords | HYDROLASE / PROTEINASE / BETA-BARREL / SERINE PROTEASE / STRUCTURAL PROTEOMICS IN EUROPE / SPINE / STRUCTURAL GENOMICS | ||||||
Function / homology | Function and homology information assemblin / viral release from host cell / host cell cytoplasm / serine-type endopeptidase activity / host cell nucleus / identical protein binding Similarity search - Function | ||||||
Biological species | HUMAN HERPESVIRUS 4 (Epstein-Barr virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Buisson, M. / Hernandez, J. / Lascoux, D. / Schoehn, G. / Forest, E. / Arlaud, G. / Seigneurin, J. / Ruigrok, R.W.H. / Burmeister, W.P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: The Crystal Structure of the Epstein-Barr Virus Protease Shows Rearrangement of the Processed C Terminus Authors: Buisson, M. / Hernandez, J. / Lascoux, D. / Schoehn, G. / Forest, E. / Arlaud, G. / Seigneurin, J. / Ruigrok, R.W.H. / Burmeister, W.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o6e.cif.gz | 100 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o6e.ent.gz | 76.8 KB | Display | PDB format |
PDBx/mmJSON format | 1o6e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/1o6e ftp://data.pdbj.org/pub/pdb/validation_reports/o6/1o6e | HTTPS FTP |
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-Related structure data
Related structure data | 1fl1S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9993, 0.0239, 0.0285), Vector: |
-Components
#1: Protein | Mass: 25423.990 Da / Num. of mol.: 2 Fragment: COAT PROTEIN VP24 (PROTEASE) DOMAIN, RESIDUES 1-235 Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN HERPESVIRUS 4 (Epstein-Barr virus) Strain: B95-8 / Cell line: B95-8 MARMOSET CELL LINE / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03234, assemblin #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | ONLY PROTEASE DOMAIN OF THE ASSEMBLIN IS PRESENT IN THE CRYSTAL.THE SEQUENCE IS MODIFIED AT THE N- ...ONLY PROTEASE DOMAIN OF THE ASSEMBLIN IS PRESENT IN THE CRYSTAL.THE SEQUENCE IS MODIFIED AT THE N-TERMINUS DUE TO THE INTRODUCTI | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52 % / Description: CRYSTAL TWINNED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 4.6 Details: HANGING DROP METHOD USING A RESERVOIR SOLUTION OF 1.25 - 1.5 M SODIUM FORMATE,100 MM SODIUM CITRATE PH4.6 5 MM EDTA, PROTEIN IN 100 MM NACL 20 MM THRIS-HCL PH 7.5 1 MM EDTA 10 MM BETA-MERCAPTOETHANOL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.919 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 15, 2001 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.919 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→45.2 Å / Num. obs: 132854 / % possible obs: 98.1 % / Redundancy: 5.4 % / Biso Wilson estimate: 56.8 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 2.3 / % possible all: 89.9 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / % possible obs: 89.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FL1 Resolution: 2.3→42 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: REFINED USING THE TWINNED TARGET, TWINNING FRACTION 0.477, OPERATOR -H,-K,L THE REFINEMENT HAS BEEN CARRIED OUT AGAINST TWINNED DATA USING THE CORRESPONDING TARGET IN CNS. R-FACTORS CAN NOT ...Details: REFINED USING THE TWINNED TARGET, TWINNING FRACTION 0.477, OPERATOR -H,-K,L THE REFINEMENT HAS BEEN CARRIED OUT AGAINST TWINNED DATA USING THE CORRESPONDING TARGET IN CNS. R-FACTORS CAN NOT DIRECTLY BE COMPARED TO THE ONES FROM UNTWINNED STRUCTURES. FOR MAP CALCULATIONS, A DIFFERENT DATASET WITH A TWINNING FRACTION MORE DIFFERENT FROM 0.5 HAS BEEN USED. ITS RESOLUTION WAS LIMITED TO 2.5 A. SOME REGIONS CARACTERISED BY B FACTORS ABOVE 90 A2 ARE POORLY DEFINED.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.6 Å2 / ksol: 0.313 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 10
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Xplor file |
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Refine LS restraints | *PLUS
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