+Open data
-Basic information
Entry | Database: PDB / ID: 1qol | ||||||
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Title | STRUCTURE OF THE FMDV LEADER PROTEASE | ||||||
Components | PROTEASE (NONSTRUCTURAL PROTEIN P20A) | ||||||
Keywords | HYDROLASE / SULFHYDRYL PROTEINASE / PICORNAVIRAL PROTEINASE | ||||||
Function / homology | Function and homology information L-peptidase / suppression by virus of host type I interferon production / modulation by virus of host chromatin organization / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / protein complex oligomerization ...L-peptidase / suppression by virus of host type I interferon production / modulation by virus of host chromatin organization / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / regulation of translation / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell endoplasmic reticulum membrane / molecular adaptor 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 / host cell nucleus / structural molecule activity / virion attachment to host cell / proteolysis / RNA binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | FOOT-AND-MOUTH DISEASE VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Guarne, A. / Tormo, J. / Kirchweger, R. / Pfistermueller, D. / Skern, T. / Fita, I. | ||||||
Citation | Journal: Embo J. / Year: 1998 Title: Structure of the Foot-and-Mouth Disease Virus Leader Protease: A Papain-Like Fold Adapted for Self-Processing and Eif4G Recognition. Authors: Guarne, A. / Tormo, J. / Kirchweger, R. / Pfistermueller, D. / Fita, I. / Skern, T. #1: Journal: J.Gen.Virol. / Year: 1998 Title: A Structural Model of Picornaviral Leader Proteinases Based on Papain and Bleomycin Hydrolase Authors: Skern, T. / Fita, I. / Guarne, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qol.cif.gz | 269.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qol.ent.gz | 226.8 KB | Display | PDB format |
PDBx/mmJSON format | 1qol.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/1qol ftp://data.pdbj.org/pub/pdb/validation_reports/qo/1qol | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | BIOCHEMICAL DATA INDICATES THAT LEADER PROTEASEIS ACTIVE AS A MONOMER. IN THE CRYSTAL ITASSOCIATES TO FORM A DIMER. |
-Components
#1: Protein | Mass: 19779.221 Da / Num. of mol.: 8 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) FOOT-AND-MOUTH DISEASE VIRUS / Strain: O1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03305 #2: Chemical | #3: Chemical | Sequence details | THE SWISSPROT ENTRY POLG_FMDVO REFERS TO A GENOME POLYPROTEIN, AND THE PROTEASE (EC 3.4.22.-) ...THE SWISSPROT ENTRY POLG_FMDVO REFERS TO A GENOME POLYPROTEI | |
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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: 3 Å3/Da / Density % sol: 58.9 % | ||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: 10% PEG 6000, 0.8 M MG CHLORIDE, 0.1 M TRIS/HCL PH=8.5, pH 8.50 | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8469 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1996 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8469 Å / Relative weight: 1 |
Reflection | Resolution: 3→34.7 Å / Num. obs: 35080 / % possible obs: 92.5 % / Redundancy: 8.4 % / Biso Wilson estimate: 63.7 Å2 / Rsym value: 0.01 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 3→3.05 Å / Mean I/σ(I) obs: 2.9 / Rsym value: 0.263 / % possible all: 74.9 |
Reflection | *PLUS Rmerge(I) obs: 0.103 |
Reflection shell | *PLUS % possible obs: 75 % / Rmerge(I) obs: 0.263 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→19.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2758596.51 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: NATIVE PATTERSON MAP PRESENT A PSEUDO-ORIGEN PEAK AT POSITION (0.5,0.5,0.225). THIS PEAK CORRESPONDS A PURE TRANSLATION THAT RELATES FOUR MOLECULES OF THE A.S.U. WITH THE OTHER FOUR
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 17 Å2 / ksol: 0.308148 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.8 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: 0.017 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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