+Open data
-Basic information
Entry | Database: PDB / ID: 1gvk | ||||||
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Title | Porcine pancreatic elastase acyl enzyme at 0.95 A resolution | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / SERINE PROTEASE / CATALYTIC INTERMEDIATE / ATOMIC RESOLUTION / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information pancreatic elastase / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | SUS SCROFA (pig) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.94 Å | ||||||
Authors | Katona, G. / Wilmouth, R.C. / Wright, P.A. / Berglund, G.I. / Hajdu, J. / Neutze, R. / Schofield, C.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: X-Ray Structure of a Serine Protease Acyl-Enzyme Complex at 0.95-A Resolution. Authors: Katona, G. / Wilmouth, R.C. / Wright, P.A. / Berglund, G.I. / Hajdu, J. / Neutze, R. / Schofield, C.J. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" 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 | 1gvk.cif.gz | 193.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gvk.ent.gz | 150.4 KB | Display | PDB format |
PDBx/mmJSON format | 1gvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gvk_validation.pdf.gz | 445.2 KB | Display | wwPDB validaton report |
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Full document | 1gvk_full_validation.pdf.gz | 448.4 KB | Display | |
Data in XML | 1gvk_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 1gvk_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/1gvk ftp://data.pdbj.org/pub/pdb/validation_reports/gv/1gvk | HTTPS FTP |
-Related structure data
Related structure data | 1qixS 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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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 368.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RELATED TO BETA-CASOMORPHIN / Source: (synth.) SYNTHETIC CONSTRUCT (others) | ||||||
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#2: Protein | Mass: 25928.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Cell: PANCREATIC ACINAR CELLS / Organ: PANCREAS / Tissue: GLAND / References: UniProt: P00772, pancreatic elastase | ||||||
#3: Chemical | #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | Compound details | ESTER BOND BETWEEN THE CATALYTIC SER195 OF ELASTASE AND ILE7 OF THE SUBSTRATE. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / pH: 5 Details: 25 MG/ML PPE, 17.5 MG/ML N-AC-NPI- CO2H, 50MM SODIUM ACETATE PH5.0, 25 MM SODIUM SULPHATE, 20 C, PH 5.00 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: used microseeding | |||||||||||||||||||||||||||||||||||
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: ESRF / Beamline: ID14-3 / Wavelength: 0.93 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 15, 2000 / Details: FOCUSING MIRRORS |
Radiation | Monochromator: DIAMOND CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 0.945→26.93 Å / Num. obs: 128075 / % possible obs: 92.7 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 0.94→0.97 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 2.1 / % possible all: 60.9 |
Reflection | *PLUS Highest resolution: 0.95 Å / Lowest resolution: 26.9 Å / Num. obs: 128641 / Num. measured all: 1038838 |
Reflection shell | *PLUS Highest resolution: 0.95 Å / % possible obs: 60.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QIX Resolution: 0.94→26.93 Å / Num. parameters: 21104 / Num. restraintsaints: 27432 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 4.2 %
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 44 / Occupancy sum hydrogen: 1686 / Occupancy sum non hydrogen: 2094.6 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.94→26.93 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.148 / Rfactor Rwork: 0.123 / Highest resolution: 0.95 Å / Lowest resolution: 26.9 Å | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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