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Yorodumi- PDB-2cmy: Crystal complex between bovine trypsin and Veronica hederifolia t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cmy | ||||||
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Title | Crystal complex between bovine trypsin and Veronica hederifolia trypsin inhibitor | ||||||
Components |
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Keywords | HYDROLASE / ACYL-ENZYME INTERMEDIATE / SERINE PROTEASE INHIBITOR / ZYMOGEN / PROTEASE / DIGESTION / METAL-BINDING / SERINE PROTEASE | ||||||
Function / homology | Function and homology information trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | BOS TAURUS (cattle) VERONICA HEDERIFOLIA (ivyleaf speedwell) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Conners, R. / Yardley, J.L. / Konarev, A. / Shewry, P. / Brady, R.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: An Unusual Helix-Turn-Helix Protease Inhibitory Motif in a Novel Trypsin Inhibitor from Seeds of Veronica (Veronica Hederifolia L.). Authors: Conners, R. / Konarev, A. / Forsyth, J. / Lovegrove, A. / Marsh, J. / Joseph-Horne, T. / Shewry, P. / Brady, R.L. | ||||||
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 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-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 | 2cmy.cif.gz | 68.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cmy.ent.gz | 50.7 KB | Display | PDB format |
PDBx/mmJSON format | 2cmy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/2cmy ftp://data.pdbj.org/pub/pdb/validation_reports/cm/2cmy | HTTPS FTP |
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-Related structure data
Related structure data | 2plxC 1sfiS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PURIFIED PROTEIN OBTAINED FROM SIGMA / Source: (natural) BOS TAURUS (cattle) / Organ: PANCREAS / References: UniProt: P00760, trypsin |
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#2: Protein/peptide | Mass: 4056.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM SEEDS / Source: (natural) VERONICA HEDERIFOLIA (ivyleaf speedwell) / Tissue: SEED / References: UniProt: P85981*PLUS |
-Non-polymers , 4 types, 114 molecules
#3: Chemical | #4: Chemical | ChemComp-CA / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | VERONICA HEDERIFOLIA TRYPSIN INHIBITOR SEQUENCE IS NOT PRESENT IN ANY SEQUENCE DATABASE. WE WILL ...VERONICA HEDERIFOLI |
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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: 2.58 Å3/Da / Density % sol: 51.96 % / Description: NONE |
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Crystal grow | pH: 8 Details: CRYSTALS OF TRYPSIN WERE GROWN IN 2.5M AMMONIUM SULPHATE, 6MM CALCIUM CHLORIDE, 0.1M TRIS PH 8.15, 60MM BENZAMIDINE. THEY WERE BACKSOAKED IN 0.1M NA PHOSPHATE PH 5.8, 2.5M AMMONIUM SULPHATE ...Details: CRYSTALS OF TRYPSIN WERE GROWN IN 2.5M AMMONIUM SULPHATE, 6MM CALCIUM CHLORIDE, 0.1M TRIS PH 8.15, 60MM BENZAMIDINE. THEY WERE BACKSOAKED IN 0.1M NA PHOSPHATE PH 5.8, 2.5M AMMONIUM SULPHATE TO REMOVE BENZAMIDINE. CRYSTALS WERE MOVED TO 2.5M AMMONIUM SULPHATE, 1MM CALCIUM CHLORDIE, 0.1M TRIS PH 8 AND PEPTIDE INHIBITOR ADDED AT 10MM AND INCUBATED FOR 16 HOURS. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 5, 2003 / Details: MIRROR |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→47.73 Å / Num. obs: 13342 / % possible obs: 97.5 % / Observed criterion σ(I): 1.4 / Redundancy: 4.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.4 / % possible all: 84.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SFI Resolution: 2.25→47.73 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.917 / SU B: 12.837 / SU ML: 0.176 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-6, 16-17 AND 30-34 OF THE VERONICA HEDERIFOLIA INHIBITOR (CHAIN B) ARE DISORDERED AND NOT INCLUDED IN THE MODEL.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.66 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→47.73 Å
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Refine LS restraints |
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