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Yorodumi- PDB-1jq7: HCMV protease dimer-interface mutant, S225Y complexed to Inhibito... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jq7 | ||||||
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Title | HCMV protease dimer-interface mutant, S225Y complexed to Inhibitor BILC 408 | ||||||
Components | ASSEMBLIN | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Herpesvirus / cytomegalovirus / serine protease / dimerization / enzyme activity regulation / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
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: 3 Å | ||||||
Authors | Batra, R. / Khayat, R. / Tong, L. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: Molecular mechanism for dimerization to regulate the catalytic activity of human cytomegalovirus protease. Authors: Batra, R. / Khayat, R. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jq7.cif.gz | 99.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jq7.ent.gz | 74.8 KB | Display | PDB format |
PDBx/mmJSON format | 1jq7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jq7_validation.pdf.gz | 538.1 KB | Display | wwPDB validaton report |
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Full document | 1jq7_full_validation.pdf.gz | 568.1 KB | Display | |
Data in XML | 1jq7_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 1jq7_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/1jq7 ftp://data.pdbj.org/pub/pdb/validation_reports/jq/1jq7 | HTTPS FTP |
-Related structure data
Related structure data | 1jq6C 2wpoS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28206.641 Da / Num. of mol.: 2 / Mutation: A143Q, S225Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 5 / Production host: Escherichia coli (E. coli) / References: UniProt: P16753, assemblin #2: Chemical | Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 717.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H63N7O7 / Details: This peptide was chemically synthesized. References: N-(6-aminohexanoyl)-3-methyl-L-valyl-3-methyl-L-valyl-N~4~,N~4~-dimethyl-N~1~-[(1R)-1-methyl-2,3-dioxo-3-{[(1S)-1- phenylpropyl]amino}propyl]-L-aspartamide Nonpolymer details | THE INHIBITOR 0FP IS COVALENTLY CONNECTED AT CARBON C4 TO THE ACTIVE SITE SERINES (A 1132 AND B ...THE INHIBITOR 0FP IS COVALENTLY | |
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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: 2.58 Å3/Da / Density % sol: 52.4 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, HEPES, sodium chloride, glycerol, spermine tetrahydrochloride, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / Details: Tong, L., (1998) Nature Struct. Biol., 5, 819. | |||||||||||||||||||||||||||||||||||||||||||||||||
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: X8C / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 2, 2001 |
Radiation | Monochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 3→19.9 Å / Num. all: 48246 / Num. obs: 10900 / % possible obs: 85.5 % / Observed criterion σ(F): 7 / Observed criterion σ(I): 5 |
Reflection shell | Resolution: 3→3.19 Å / % possible all: 97 |
Reflection | *PLUS Num. measured all: 48246 / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS Rmerge(I) obs: 0.129 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WPO (dimer) Resolution: 3→19.99 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 2061042.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 7 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.250918 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.037 / 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): 7 / % reflection Rfree: 7.4 % / Rfactor obs: 0.26 / Rfactor Rwork: 0.26 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.36 / % reflection Rfree: 7.5 % / Rfactor Rwork: 0.281 |