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Yorodumi- PDB-2j9n: Robotically harvested Trypsin complexed with Benzamidine containi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j9n | ||||||
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Title | Robotically harvested Trypsin complexed with Benzamidine containing polypeptide mediated crystal contacts | ||||||
Components |
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Keywords | HYDROLASE / ROBOTIC HARVEST / INTERMOLECULAR CONTACTS / TRYPSIN / CALCIUM / ZYMOGEN / PROTEASE / DIGESTION / SALMON PROTAMINE PEPTIDES / BENZAMIDINE / METAL-BINDING / SERINE PROTEASE | ||||||
Function / homology | Function and homology information trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | BOS TAURUS (cattle) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Viola, R. / Carman, P. / Walsh, J. / Miller, E. / Benning, M. / Frankel, D. / McPherson, A. / Cudney, R. / Rupp, B. | ||||||
Citation | Journal: J.Appl.Crystallogr. / Year: 2007 Title: Operator Assisted Harvesting of Protein Crystals Using a Universal Micromanipulation Robot. Authors: Viola, R. / Carman, P. / Walsh, J. / Miller, E. / Benning, M. / Frankel, D. / McPherson, A. / Cudney, R. / Rupp, B. | ||||||
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 | 2j9n.cif.gz | 68.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j9n.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 2j9n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/2j9n ftp://data.pdbj.org/pub/pdb/validation_reports/j9/2j9n | HTTPS FTP |
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-Related structure data
Related structure data | 1y5bS 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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Details | THE ENTRY ALSO CONTAINS TWO SHORT PEPTIDE CHAINS OF UNKNOWN SEQUENCE. THE TRYPSIN MOLECULE IS MONOMERICIN SOLUTION. |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-243 / Source method: isolated from a natural source / Details: SIGMA / Source: (natural) BOS TAURUS (cattle) / Organ: PANCREAS / Tissue: SMOOTH / References: UniProt: P00760, trypsin |
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-Protein/peptide , 2 types, 2 molecules BC
#2: Protein/peptide | Mass: 1294.587 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
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#3: Protein/peptide | Mass: 316.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
-Non-polymers , 5 types, 212 molecules
#4: Chemical | ChemComp-CA / |
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#5: Chemical | ChemComp-NA / |
#6: Chemical | ChemComp-BEN / |
#7: Chemical | ChemComp-IPH / |
#8: 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: 2.03 Å3/Da / Density % sol: 39.1 % / Description: NONE |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: STOCK: 60 MG BOVINE TRYPSIN (SIGMA) PLUS 5 MG BENZAMIDINE (SIGMA) IN 1 ML OF HEPES BUFFER 0.1M PH 7.0 AND 3 MM CACL2. COCKTAIL: 15% PEG 3350 IN 0.1 M HEPES PH 7.0 ALSO CONTAINING 10 MG/ML ...Details: STOCK: 60 MG BOVINE TRYPSIN (SIGMA) PLUS 5 MG BENZAMIDINE (SIGMA) IN 1 ML OF HEPES BUFFER 0.1M PH 7.0 AND 3 MM CACL2. COCKTAIL: 15% PEG 3350 IN 0.1 M HEPES PH 7.0 ALSO CONTAINING 10 MG/ML SALMON SPERM PROTAMINE (SIGMA) DROP: 2 UL STOCK PLUS 2 UL COCKTAIL IN CRYSCHEM PLATES AT 22 DEG C. |
-Data collection
Diffraction | Mean temperature: 125 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54178 |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Aug 3, 2006 / Details: MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→25.09 Å / Num. obs: 31641 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 7.46 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.37 |
Reflection shell | Resolution: 1.5→1.57 Å / Redundancy: 3.32 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.84 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Y5B Resolution: 1.5→25.09 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.134 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. WARNING: THE PEPTIDES B AND C MEDIATING INTERMOLECULAR CONTACTS BETWEEN 3 TRYPSIN MONOMERS HAVE BEEN ASSIGNED RESIDUE TYPE UNK. THEY HAVE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. WARNING: THE PEPTIDES B AND C MEDIATING INTERMOLECULAR CONTACTS BETWEEN 3 TRYPSIN MONOMERS HAVE BEEN ASSIGNED RESIDUE TYPE UNK. THEY HAVE HIGH B-FACTORS AND ARE INTENDED AS PLACE HOLDERS FOR WHAT WE BELIEVE IS A MIXTURE OF BASIC PROTAMINE PEPTIDES, POLYAMINES, AND OTHER COMPOUNDS FROM THE SALMON PROTAMINE EXTRACT, PROBABLY IN MULTIPLE CONFORMATIONS. SIMILAR CAVEATS APPLY TO THE PHENOL ENTITIES WE BELIEVE ORIGINATE FROM IMPURITIES IN THE PROTAMINE EXTRACT USED AS A CRYSTALLIZATION ADDITIVE.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.45 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→25.09 Å
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Refine LS restraints |
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