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Open data
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Basic information
Entry | Database: PDB / ID: 1jq6 | ||||||
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Title | HUMAN CYTOMEGALOVIRUS PROTEASE DIMER-INTERFACE MUTANT, S225Y | ||||||
![]() | ASSEMBLIN | ||||||
![]() | HYDROLASE / Herpesvirus / cytomegalovirus / serine protease / dimerization / enzyme activity regulation | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Batra, R. / Khayat, R. / Tong, L. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.2 KB | Display | ![]() |
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PDB format | ![]() | 33.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 370.3 KB | Display | ![]() |
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Full document | ![]() | 372.6 KB | Display | |
Data in XML | ![]() | 5.3 KB | Display | |
Data in CIF | ![]() | 7.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jq7C ![]() 1wpoS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | Monomer in the asymmetric unit, but biological assembly unit is a dimer that can be generated by the two fold axis. |
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Components
#1: Protein | Mass: 28518.590 Da / Num. of mol.: 1 / Mutation: A143Q, S225Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.47 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: PEG 8000, sodium cacodylate, magnesium acetate, glycerol, spermine tetrahydrochloride, DTT, pH 7.2, VAPOR DIFFUSION, SITTING 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: ![]() ![]() ![]() |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Nov 9, 2000 |
Radiation | Monochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→19.3 Å / Num. all: 38153 / Num. obs: 10420 / % possible obs: 91 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 18.5 Å2 |
Reflection shell | Resolution: 2.3→2.44 Å / % possible all: 93 |
Reflection | *PLUS % possible obs: 91 % / Num. measured all: 38153 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS Rmerge(I) obs: 0.172 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1WPO (monomer) Resolution: 2.3→19.3 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 5293688.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.4329 Å2 / ksol: 0.394661 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→19.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.026 / 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: 7.6 % / Rfactor obs: 0.229 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 43.2 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.284 / % reflection Rfree: 7.5 % / Rfactor Rwork: 0.249 |