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- PDB-2bd8: Porcine pancreatic elastase complexed with beta-casomorphin-7 and... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bd8 | ||||||
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Title | Porcine pancreatic elastase complexed with beta-casomorphin-7 and Arg-Phe at pH 5.0 (50 min soak) and immersed in pH 9 buffer for 30 seconds | ||||||
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![]() | 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.8 KB | Display | ![]() |
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PDB format | ![]() | 45.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2bb4C ![]() 2bd2C ![]() 2bd3C ![]() 2bd4C ![]() 2bd5C ![]() 2bd7C ![]() 2bd9C ![]() 2bdaC ![]() 2bdbC ![]() 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
-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) ![]() ![]() |
-Non-polymers , 5 types, 131 molecules ![](data/chem/img/ARG.gif)
![](data/chem/img/PHE.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PHE.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ARG / |
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#4: Chemical | ChemComp-PHE / |
#5: Chemical | ChemComp-CA / |
#6: Chemical | ChemComp-SO4 / |
#7: Water | ChemComp-HOH / |
-Details
Nonpolymer details | OG SER A 195, C ILE P 7 AND N ARG P 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.6 % |
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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 ARG-PHE (2 MG) IN 250MM SODIUM ACETATE (PH 5.0) (5 MICROLITRES) FOR 50 MIN, VAPOR ...Details: 25MM SODIUM SULPHATE, 25MM SODIUM ACETATE (PH 5.0), 25 MG/ML PPE AND 17.5 MG/ML BCM7, AND THEN SOAKED WITH ARG-PHE (2 MG) IN 250MM SODIUM ACETATE (PH 5.0) (5 MICROLITRES) FOR 50 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: Jul 2, 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→19.7 Å / Num. obs: 24742 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 5.3 / Num. unique all: 3539 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3EST Resolution: 1.7→19.7 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.123 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: The PPE:BCM7:ARG-PHE PH 5 (50 min soak) crystal (from which PDB file 2BD7 was collected) was warmed to room temperature, immersed in 250 mm ches PH 9, 25% (v/v) glycerol for 30s and refrozen.
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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: 27.949 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→19.7 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: -4.224 Å / Origin y: 28.209 Å / Origin z: 43.005 Å
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Refinement TLS group | Selection: ALL |