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Yorodumi- PDB-1hb0: Snapshots of serine protease catalysis: (D) acyl-enzyme intermedi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hb0 | ||||||
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Title | Snapshots of serine protease catalysis: (D) acyl-enzyme intermediate between porcine pancreatic elastase and human beta-casomorphin-7 jumped to pH 10 for 2 minutes | ||||||
Components | ELASTASE 1 | ||||||
Keywords | HYDROLASE / SERINE PROTEINASE / 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: 2.05 Å | ||||||
Authors | Wilmouth, R.C. / Edman, K. / Neutze, R. / Wright, P.A. / Clifton, I.J. / Schneider, T.R. / Schofield, C.J. / Hajdu, J. | ||||||
Citation | 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. #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: Acta Crystallogr.,Sect.B / Year: 1988 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hb0.cif.gz | 63.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hb0.ent.gz | 45.3 KB | Display | PDB format |
PDBx/mmJSON format | 1hb0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hb0_validation.pdf.gz | 426.5 KB | Display | wwPDB validaton report |
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Full document | 1hb0_full_validation.pdf.gz | 427.9 KB | Display | |
Data in XML | 1hb0_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 1hb0_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/1hb0 ftp://data.pdbj.org/pub/pdb/validation_reports/hb/1hb0 | HTTPS FTP |
-Related structure data
Related structure data | 1haxC 1hayC 1hazC 1qixS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 26014.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: PANCREAS / References: UniProt: P00772, EC: 3.4.21.11 |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.78 Å3/Da / Density % sol: 30.3 % | |||||||||||||||||||||||||
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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: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.99 |
Detector | Type: PRINCETON / Detector: CCD / Date: Jan 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→26.8 Å / Num. obs: 12678 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 6.8 / % possible all: 85.9 |
Reflection | *PLUS Num. measured all: 130629 |
Reflection shell | *PLUS % possible obs: 85.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QIX Resolution: 2.05→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: 50.3 Å2 / ksol: 0.42 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.12 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.28 |