+Open data
-Basic information
Entry | Database: PDB / ID: 1at3 | ||||||
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Title | HERPES SIMPLEX VIRUS TYPE II PROTEASE | ||||||
Components | HERPES SIMPLEX VIRUS TYPE II PROTEASE | ||||||
Keywords | SERINE PROTEASE / VIRAL PROTEASE / HSV2 PROTEASE | ||||||
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 2 | ||||||
Method | X-RAY DIFFRACTION / molecular replacement, MIR / Resolution: 2.5 Å | ||||||
Authors | Hoog, S. / Smith, W.W. / Qiu, X. / Abdel-Meguid, S.S. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Active site cavity of herpesvirus proteases revealed by the crystal structure of herpes simplex virus protease/inhibitor complex. Authors: Hoog, S.S. / Smith, W.W. / Qiu, X. / Janson, C.A. / Hellmig, B. / McQueney, M.S. / O'Donnell, K. / O'Shannessy, D. / DiLella, A.G. / Debouck, C. / Abdel-Meguid, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1at3.cif.gz | 90.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1at3.ent.gz | 72.5 KB | Display | PDB format |
PDBx/mmJSON format | 1at3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1at3_validation.pdf.gz | 391.5 KB | Display | wwPDB validaton report |
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Full document | 1at3_full_validation.pdf.gz | 404.3 KB | Display | |
Data in XML | 1at3_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 1at3_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/1at3 ftp://data.pdbj.org/pub/pdb/validation_reports/at/1at3 | HTTPS FTP |
-Related structure data
Related structure data | 1vzvS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper: (Code: given Matrix: (0.931609, 0.05004, 0.36), Vector: |
-Components
#1: Protein | Mass: 27055.979 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: DIISOPROPYL PHOSPHATE COVALENTLY BOUND TO ACTIVE SITE SER 129 Source: (gene. exp.) Human herpesvirus 2 / Genus: Simplexvirus / Production host: Escherichia coli (E. coli) / References: UniProt: Q69527 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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 % | ||||||||||||||||||
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Crystal grow | pH: 5 / Details: 10% PEG4000, PH 5.0 | ||||||||||||||||||
Crystal | *PLUS Density % sol: 45 % | ||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1996 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→25 Å / Num. obs: 78502 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.5→2.61 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3 / Rsym value: 0.24 / % possible all: 88 |
Reflection | *PLUS Num. obs: 15788 / Num. measured all: 78502 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement, MIR Starting model: 1VZV Resolution: 2.5→10 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 21.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.5→2.61 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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