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- PDB-2bdb: Porcine pancreatic elastase complexed with Asn-Pro-Ile and Ala-Al... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bdb | ||||||
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Title | Porcine pancreatic elastase complexed with Asn-Pro-Ile and Ala-Ala at pH 5.0 | ||||||
![]() | Elastase-1 | ||||||
![]() | HYDROLASE / SERINE PROTEINASE | ||||||
Function / homology | ![]() pancreatic elastase / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Liu, B. / Schofield, C.J. / Wilmouth, R.C. | ||||||
![]() | ![]() Title: Structural analyses on intermediates in serine protease catalysis Authors: Liu, B. / Schofield, C.J. / Wilmouth, R.C. #1: ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.7 KB | Display | ![]() |
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PDB format | ![]() | 44.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.7 KB | Display | ![]() |
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Full document | ![]() | 443.3 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bb4C ![]() 2bd2C ![]() 2bd3C ![]() 2bd4C ![]() 2bd5C ![]() 2bd7C ![]() 2bd8C ![]() 2bd9C ![]() 2bdaC ![]() 2bdcC ![]() 2h1uC ![]() 3estS ![]() 2bd6 C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25928.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||
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#2: Chemical | ChemComp-CA / | ||||
#3: Chemical | ChemComp-SO4 / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THIS CONFLICT IS BASED ON THE REFERENCE 3 IN SEQUENCE DATABASE, P00772 IN SWISS-PROT. | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.93 % |
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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 NPI, 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 NPI, 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: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 16, 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: 1.7→17.46 Å / Num. obs: 24480 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 8.2 / Num. unique all: 3493 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3EST Resolution: 1.7→17.46 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.099 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: The peptide ASN-PRO-ILE was not modelled into the structure.
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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: 17.222 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→17.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -4.2239 Å / Origin y: 28.18 Å / Origin z: 42.7847 Å
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Refinement TLS group | Selection: ALL |