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Yorodumi- PDB-1oyv: Crystal structure of tomato inhibitor-II in a ternary complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oyv | ||||||
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Title | Crystal structure of tomato inhibitor-II in a ternary complex with subtilisin Carlsberg | ||||||
Components |
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Keywords | HYDROLASE / serine proteinase inhibitor / ternary complex / multidomain inhibitor / potato II family | ||||||
Function / homology | Function and homology information subtilisin / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus licheniformis (bacteria) Solanum lycopersicum (tomato) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Barrette-Ng, I.H. / Ng, K.K. / Cherney, M.M. / Pearce, G. / Ryan, C.A. / James, M.N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Structural basis of inhibition revealed by a 1:2 complex of the two-headed tomato inhibitor-II and subtilisin Carlsberg Authors: Barrette-Ng, I.H. / Ng, K.K. / Cherney, M.M. / Pearce, G. / Ryan, C.A. / James, M.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oyv.cif.gz | 129.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oyv.ent.gz | 99.9 KB | Display | PDB format |
PDBx/mmJSON format | 1oyv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/1oyv ftp://data.pdbj.org/pub/pdb/validation_reports/oy/1oyv | HTTPS FTP |
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-Related structure data
Related structure data | 1scnS 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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Unit cell |
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-Components
#1: Protein | Mass: 27306.199 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bacillus licheniformis (bacteria) / Strain: Nagarse / References: UniProt: P00780, subtilisin #2: Protein | | Mass: 13468.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: leaves of tomato plant / Source: (natural) Solanum lycopersicum (tomato) / Strain: Bonny Best / References: UniProt: P05119 #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.55 Å3/Da / Density % sol: 51.39 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 8000, sodium malonate, sodium citrate, ethylene glycol, ethanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: used macroseeding | ||||||||||||||||||||||||||||||||||||
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: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 2002 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. all: 23099 / % possible obs: 98.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2173 / Rsym value: 0.473 / % possible all: 94.1 |
Reflection | *PLUS Num. obs: 23099 / Num. measured all: 97405 |
Reflection shell | *PLUS % possible obs: 94.1 % / Num. unique obs: 2173 / Num. measured obs: 7394 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SCN Resolution: 2.5→40 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 32.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.27 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS |