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Yorodumi- PDB-2bd3: Porcine pancreatic elastase complexed with beta-casomorphin-7 and... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bd3 | ||||||
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Title | Porcine pancreatic elastase complexed with beta-casomorphin-7 and Lys-Ala-NH2 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 / MOLECULAR REPLACEMENT / Resolution: 1.6 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bd3.cif.gz | 65.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bd3.ent.gz | 45.9 KB | Display | PDB format |
PDBx/mmJSON format | 2bd3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/2bd3 ftp://data.pdbj.org/pub/pdb/validation_reports/bd/2bd3 | HTTPS FTP |
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-Related structure data
Related structure data | 2bb4C 2bd2C 2bd4C 2bd5C 2bd7C 2bd8C 2bd9C 2bdaC 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: 863.995 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 , 5 types, 133 molecules
#3: Chemical | ChemComp-LYS / |
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#4: Chemical | ChemComp-CA / |
#5: Chemical | ChemComp-SO4 / |
#6: Chemical | ChemComp-ALA / |
#7: Water | ChemComp-HOH / |
-Details
Nonpolymer details | OG SER A 195, C ILE P 7 AND N LYS 1001 ARE COVALENTLYSequence details | THIS CONFLICT IS BASED ON THE REFERENCE 3 IN SEQUENCE DATABASE, P00772 IN SWISS-PROT. | |
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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: 2.03 Å3/Da / Density % sol: 39.55 % |
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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 BCM7, AND THEN SOAKED WITH Lys-Ala-NH2 (50MG/ML) IN 250MM SODIUM ACETATE (PH 5.0) (5 MICROLITRES) FOR 30 MIN, ...Details: 25MM SODIUM SULPHATE, 25MM SODIUM ACETATE (PH 5.0), 25 MG/ML PPE AND 17.5 MG/ML BCM7, AND THEN SOAKED WITH Lys-Ala-NH2 (50MG/ML) 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 18, 2005 / Details: OSMIC mirrors |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.6→18.9 Å / Num. obs: 29238 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 28.7 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 11.8 / Num. unique all: 4135 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3EST Resolution: 1.6→18.9 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.742 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.088 / 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: 23.238 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→18.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -4.193 Å / Origin y: 28.275 Å / Origin z: 42.997 Å
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Refinement TLS group | Selection: ALL |