+Open data
-Basic information
Entry | Database: PDB / ID: 4v0t | ||||||
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Title | Monomeric pseudorabies virus protease pUL26N at 2.1 A resolution | ||||||
Components | UL26 | ||||||
Keywords | HYDROLASE / ASSEMBLIN / SERINE PROTEASE / PROTEASE / SUID / PRV / HERPES / HERPES VIRUS | ||||||
Function / homology | Function and homology information assemblin / viral release from host cell / host cell cytoplasm / serine-type endopeptidase activity / host cell nucleus / proteolysis / identical protein binding Similarity search - Function | ||||||
Biological species | SUID HERPESVIRUS 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Zuehlsdorf, M. / Werten, S. / Palm, G.J. / Hinrichs, W. | ||||||
Citation | Journal: Plos Pathog. / Year: 2015 Title: Dimerization-Induced Allosteric Changes of the Oxyanion-Hole Loop Activate the Pseudorabies Virus Assemblin Pul26N, a Herpesvirus Serine Protease Authors: Zuehlsdorf, M. / Werten, S. / Klupp, B.G. / Palm, G.J. / Mettenleiter, T. / Hinrichs, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v0t.cif.gz | 183.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4v0t.ent.gz | 149.5 KB | Display | PDB format |
PDBx/mmJSON format | 4v0t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v0/4v0t ftp://data.pdbj.org/pub/pdb/validation_reports/v0/4v0t | HTTPS FTP |
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-Related structure data
Related structure data | 4cx8C 4v07SC 4v08C C: citing same article (ref.) 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 oper: (Code: given Matrix: (0.6105, -0.1704, -0.7735), Vector: |
-Components
#1: Protein | Mass: 26645.357 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-224 Source method: isolated from a genetically manipulated source Details: N-TERMINAL (HIS)6-TAG WITH THROMBIN-LINKER / Source: (gene. exp.) SUID HERPESVIRUS 1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83417, assemblin #2: Water | ChemComp-HOH / | Sequence details | ASSEMBLIN-PART CRYSTALLIZ | |
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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: 2.44 Å3/Da / Density % sol: 49.62 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 0.1 M TRIS/HCL PH 8, 8% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2014 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→78.8 Å / Num. obs: 33525 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 43.97 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.33 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.69 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4V07 Resolution: 2.05→78.81 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.94 / SU B: 9.117 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. RESIDUES 15,20,46,79,189 AND 198 OF CHAIN A AND RESIDUES 19,46,156,165,172,185,189,192,193,199,202, ,206 AND 218 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. RESIDUES 15,20,46,79,189 AND 198 OF CHAIN A AND RESIDUES 19,46,156,165,172,185,189,192,193,199,202, ,206 AND 218 OF CHAIN B MODELED AS ALA AND RESIDUE 44 FROM CHAIN A SHORTENED DUE TO INSUFFICIENT ELECTRON DENSITY, TAG WITH THROMBIN -LINKER OF BOTH CHAINS AND RESIDUES 16- -19 OF CHAIN A AND RESIDUES 14-18,194-196 AND 224 OF CHAIN B ARE DISORDERED
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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: 51.487 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→78.81 Å
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