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Yorodumi- PDB-2bda: Porcine pancreatic elastase complexed with N-acetyl-NPI and Ala-A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bda | ||||||
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Title | Porcine pancreatic elastase complexed with N-acetyl-NPI and Ala-Ala at pH 5.0 | ||||||
Components |
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Keywords | HYDROLASE / SERINE PROTEINASE | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Liu, B. / Schofield, C.J. / Wilmouth, R.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Structural analyses on intermediates in serine protease catalysis Authors: Liu, B. / Schofield, C.J. / Wilmouth, R.C. #1: Journal: Nat.Struct.Biol. / Year: 1997 Title: Structure of a specific acyl-enzyme complex formed between beta-casomorphin-7 and porcine pancreatic elastase Authors: Wilmouth, R.C. / Clifton, I.J. / Robinson, C.V. / Roach, P.L. / Aplin, R.T. / Westwood, N.J. / Hajdu, J. / Schofield, C.J. #2: Journal: Nat.Struct.Biol. / Year: 2001 Title: X-ray snapshots of serine protease catalysis reveal a tetrahedral intermediate Authors: Wilmouth, R.C. / Edman, K. / Neutze, R. / Wright, P.A. / Clifton, I.J. / Schneider, T.R. / Schofield, C.J. / Hajdu, J. #3: 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bda.cif.gz | 64.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bda.ent.gz | 45.4 KB | Display | PDB format |
PDBx/mmJSON format | 2bda.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/2bda ftp://data.pdbj.org/pub/pdb/validation_reports/bd/2bda | HTTPS FTP |
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-Related structure data
Related structure data | 2bb4C 2bd2C 2bd3C 2bd4C 2bd5C 2bd7C 2bd8C 2bd9C 2bdbC 2bdcC 2h1uC 3estS 2bd6 C: citing same article (ref.) 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
-Protein/peptide / Protein , 2 types, 2 molecules PA
#1: Protein/peptide | Mass: 342.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide |
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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) / References: UniProt: P00772, pancreatic elastase |
-Non-polymers , 4 types, 124 molecules
#3: Chemical | #4: Chemical | ChemComp-CA / | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | OG SER A 195, C ILE P 7 AND N ALA P 1001 ARE COVALENTLYSequence details | THIS CONFLICT IS BASED ON THE REFERENCE 3 IN SEQUENCE DATABASE, P00772 IN SWISS-PROT. THE PEPTIDE ...THIS CONFLICT IS BASED ON THE REFERENCE 3 IN SEQUENCE DATABASE, P00772 IN SWISS-PROT. THE PEPTIDE CHAIN P HAS ACETYLATIO | |
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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: 2.04 Å3/Da / Density % sol: 39.85 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 25MM SODIUM SULPHATE, 25MM SODIUM ACETATE (PH 5.0), 25 MG/ML PPE AND 17.5 MG/ML AcNPI, AND THEN SOAKED WITH ALA-ALA (2 MG) IN 250MM SODIUM ACETATE (PH 5.0) (5 MICROLITRES) FOR 30 MIN, VAPOR ...Details: 25MM SODIUM SULPHATE, 25MM SODIUM ACETATE (PH 5.0), 25 MG/ML PPE AND 17.5 MG/ML AcNPI, AND THEN SOAKED WITH ALA-ALA (2 MG) IN 250MM SODIUM ACETATE (PH 5.0) (5 MICROLITRES) FOR 30 MIN, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 127 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 2, 2005 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19.6 Å / Num. obs: 20470 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2950 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3EST Resolution: 1.8→19.6 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.434 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.773 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -4.272 Å / Origin y: 28.184 Å / Origin z: 42.571 Å
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Refinement TLS group | Selection: ALL |