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Yorodumi- PDB-2j92: 3C PROTEASE FROM TYPE A10(61) FOOT-AND-MOUTH DISEASE VIRUS - Crys... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j92 | ||||||
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Title | 3C PROTEASE FROM TYPE A10(61) FOOT-AND-MOUTH DISEASE VIRUS - Crystal packing mutant (K51Q) | ||||||
Components | PICORNAIN 3C | ||||||
Keywords | HYDROLASE / FOOT-AND- MOUTH DISEASE VIRUS / CHYMOTRYPSIN-LIKE CYSTEINE PROTEASE / THIOL PROTEASE / RNA REPLICATION | ||||||
Function / homology | Function and homology information L-peptidase / modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / regulation of translation / protein complex oligomerization ...L-peptidase / modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / regulation of translation / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | FOOT-AND-MOUTH DISEASE VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Sweeney, T.R. / Birtley, J.R. / Leatherbarrow, R.J. / Curry, S. | ||||||
Citation | Journal: J.Virol. / Year: 2007 Title: Structural and Mutagenic Analysis of Foot-and-Mouth Disease Virus 3C Protease Reveals the Role of the {Beta}-Ribbon in Proteolysis. Authors: Sweeney, T.R. / Roque-Rosell, N. / Birtley, J.R. / Leatherbarrow, R.J. / Curry, S. #1: Journal: J.Biol.Chem. / Year: 2005 Title: Crystal Structure of Foot-and-Mouth Disease Virus 3C Protease: New Insights Into Catalytic Mechanism and Cleavage Specificity Authors: Birtley, J.R. / Knox, S.R. / Jaulent, A.M. / Brick, P. / Leatherbarrow, R.J. / Curry, S. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 12-STRANDED BARREL THIS IS REPRESENTED BY A 13-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j92.cif.gz | 85.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j92.ent.gz | 64 KB | Display | PDB format |
PDBx/mmJSON format | 2j92.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/2j92 ftp://data.pdbj.org/pub/pdb/validation_reports/j9/2j92 | HTTPS FTP |
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-Related structure data
Related structure data | 2bhgS 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: (-0.9227, 0.3129, 0.2253), Vector: |
-Components
#1: Protein | Mass: 22518.006 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: K51Q - TO DISRUPT ORIGINAL CRYSTAL PACKING C95K - TO AVOID AGGREGATION C142S - TO AVOID AGGREGATION C163A - TO REMOVE ACITVE-STE NUCLEOPHILE. Source: (gene. exp.) FOOT-AND-MOUTH DISEASE VIRUS (STRAIN A10-61) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03306, picornain 3C #2: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, LYS 1700 TO GLN ENGINEERED RESIDUE IN CHAIN A, CYS 1744 TO LYS ...ENGINEERED | Sequence details | THE CONFLICT ASN1671 (ILE22) ARISES PROBABLY BECAUSE OF A SEQUENCING ERROR IN THE P03306 ENTRY. ...THE CONFLICT ASN1671 (ILE22) ARISES PROBABLY BECAUSE OF A SEQUENCING | |
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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: 2.4 Å3/Da / Density % sol: 48.36 % |
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Crystal grow | pH: 7 / Details: SEE PAPER, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 15, 2005 Details: RH COATED COLLIMATING MIRROR, A DOUBLE CRYSTAL SI(III) MONOCHROMATOR WITH HORIZONTAL SAGGITAL FOCUSING SYSTEM, AND FINALLY A SECOND RH COATED MIRROR FOR VERTICAL FOCUSING. |
Radiation | Monochromator: DOUBLE CRYSTAL SI(III) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→23.6 Å / Num. obs: 20590 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.8 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BHG Resolution: 2.2→23.59 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1483613.08 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.3037 Å2 / ksol: 0.329538 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→23.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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