+Open data
-Basic information
Entry | Database: PDB / ID: 1c8o | ||||||
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Title | 2.9 A STRUCTURE OF CLEAVED VIRAL SERPIN CRMA | ||||||
Components | (ICE INHIBITOR) x 2 | ||||||
Keywords | VIRAL PROTEIN / SERPIN FOLD | ||||||
Function / homology | Function and homology information : / Microbial modulation of RIPK1-mediated regulated necrosis / cysteine-type endopeptidase inhibitor activity / protein sequestering activity / Regulation of TNFR1 signaling / serine-type endopeptidase inhibitor activity / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / host cell cytoplasm / extracellular space / cytoplasm Similarity search - Function | ||||||
Biological species | Cowpox virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å | ||||||
Authors | Simonovic, M. / Gettins, P.G.W. / Volz, K. | ||||||
Citation | Journal: Protein Sci. / Year: 2000 Title: Crystal structure of viral serpin crmA provides insights into its mechanism of cysteine proteinase inhibition. Authors: Simonovic, M. / Gettins, P.G.W. / Volz, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c8o.cif.gz | 75.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c8o.ent.gz | 56.8 KB | Display | PDB format |
PDBx/mmJSON format | 1c8o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/1c8o ftp://data.pdbj.org/pub/pdb/validation_reports/c8/1c8o | HTTPS FTP |
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-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: 33465.551 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-300 / Mutation: C93S,C102S,C124S,C223S,C269S,C298S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cowpox virus / Genus: Orthopoxvirus / Description: VIRUS; / Plasmid: PQE60 / Production host: Escherichia coli (E. coli) / References: UniProt: P07385 |
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#2: Protein/peptide | Mass: 4517.984 Da / Num. of mol.: 1 / Fragment: RESIDUES 301-341 / Mutation: C304S,C313S,C336S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cowpox virus / Genus: Orthopoxvirus / Plasmid: PQE60 / Production host: Escherichia coli (E. coli) / References: UniProt: P07385 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.72 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: sodium/potassium phosphate 1.6M, pH 5.4, vapor diffusion/hanging drop, temperature 298K | ||||||||||||||||||||
Crystal | *PLUS Density % sol: 56 % | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
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: APS / Beamline: 14-BM-C / Wavelength: 1 |
Detector | Type: ADSC / Detector: CCD / Date: Feb 7, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 9406 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.42 / Num. unique all: 930 / % possible all: 91.1 |
Reflection | *PLUS Num. obs: 9406 / Num. measured all: 318152 |
Reflection shell | *PLUS % possible obs: 91.1 % / Mean I/σ(I) obs: 4.9 |
-Processing
Software |
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Refinement | Resolution: 2.9→38.79 Å / Rfactor Rfree error: 0.009 / Data cutoff high rms absF: 335401.38 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS
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Solvent computation | Solvent model: flat model / Bsol: 44.8062 Å2 / ksol: 0.437705 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→38.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.027 / 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): 0 / % reflection Rfree: 10.5 % / Rfactor obs: 0.224 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 36.7 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.348 / % reflection Rfree: 12.1 % / Rfactor Rwork: 0.299 |