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Yorodumi- PDB-1id4: CRYSTAL STRUCTURE OF THE CATALYTIC SITE MUTANT (H157Q) OF THE HUM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1id4 | ||||||
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Title | CRYSTAL STRUCTURE OF THE CATALYTIC SITE MUTANT (H157Q) OF THE HUMAN CYTOMEGALOVIRUS PROTEASE | ||||||
Components | CAPSID PROTEIN P40: ASSEMBLIN PROTEASE | ||||||
Keywords | HYDROLASE / COAT PROTEIN / SERINE PROTEASE / PHOSPHORYLATION / VIRAL PROTEASE | ||||||
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 | Human herpesvirus 5 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Khayat, R. / Batra, R. / Massariol, M.J. / Lagace, L. / Tong, L. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Investigating the role of histidine 157 in the catalytic activity of human cytomegalovirus protease. Authors: Khayat, R. / Batra, R. / Massariol, M.J. / Lagace, L. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1id4.cif.gz | 98.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1id4.ent.gz | 75.8 KB | Display | PDB format |
PDBx/mmJSON format | 1id4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1id4_validation.pdf.gz | 375.2 KB | Display | wwPDB validaton report |
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Full document | 1id4_full_validation.pdf.gz | 384.9 KB | Display | |
Data in XML | 1id4_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 1id4_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/1id4 ftp://data.pdbj.org/pub/pdb/validation_reports/id/1id4 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28120.529 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-256 / Mutation: A143Q, H157Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 5 / Genus: Cytomegalovirus / Strain: AD169 / Gene: UL80 / Production host: Escherichia coli (E. coli) / References: UniProt: P16753, assemblin #2: 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: 2.18 Å3/Da / Density % sol: 43.66 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 19% PEG 3350, 0.1M MES 6.0, 15% Glycerol, 5% t-BuOH, 0.4M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: NSLS / Beamline: X4A / Wavelength: 0.9791 Å |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Mar 13, 2000 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 26188 / Num. obs: 25683 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 4.01 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 2.2→2.34 Å / Redundancy: 3.76 % / Rmerge(I) obs: 0.138 / % possible all: 94.9 |
Reflection | *PLUS Num. measured all: 66653 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.74 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2600390.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.92 Å2 / ksol: 0.385 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 7.3 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30.9 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.262 / % reflection Rfree: 7.2 % / Rfactor Rwork: 0.22 |