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- PDB-1hay: Snapshots of serine protease catalysis: (B) acyl-enzyme intermedi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1hay | ||||||
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Title | Snapshots of serine protease catalysis: (B) acyl-enzyme intermediate between porcine pancreatic elastase and human beta-casomorphin-7 jumped to pH 10 for 10 seconds | ||||||
![]() | ELASTASE 1![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wilmouth, R.C. / Edman, K. / Neutze, R. / Wright, P.A. / Clifton, I.J. / Schneider, T.R. / Schofield, C.J. / Hajdu, J. | ||||||
![]() | ![]() 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. #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: Structure of Native Porcine Pancreatic Elastase at 1.65A Resolution Authors: Meyer, E. / Cole, G. / Radhakrishnan, R. / Epp, O. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "B" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "B" 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64 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 | ![]() 1haxC ![]() 1hazC ![]() 1hb0C ![]() 1qixS S: Starting model for refinement C: citing same article ( |
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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: 26014.148 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: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.79 Å3/Da / Density % sol: 30.83 % | |||||||||||||||||||||||||
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Crystal grow![]() | pH: 10 Details: CRYSTALLISED FROM 25MM SODIUM SULPHATE, 25MM SODIUM ACETATE (PH 5.0), 25 MG/ML PPE AND 25 MG/ML BCM7. | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / pH: 5 / Method: vapor diffusion, hanging drop / Details: Wilmouth, R.C., (1997) Nat.Struct.Biol., 4, 456. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.7→37.7 Å / Num. obs: 23364 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 3.7 / % possible all: 91 |
Reflection | *PLUS Num. measured all: 264210 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 91 % |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1QIX Resolution: 1.7→38 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: ARG B 61 AND ARG B 125, SIDE CHAIN DISORDERED
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Solvent computation | Solvent model: STANDARD CNS / Bsol: 42.3 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.9 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.73 Å / Total num. of bins used: 19
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.34 |