+Open data
-Basic information
Entry | Database: PDB / ID: 1pq8 | ||||||
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Title | Trypsin at pH 4 at atomic resolution | ||||||
Components |
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Keywords | HYDROLASE / trypsin / atomic resolution / catalysis | ||||||
Function / homology | Function and homology information trypsin / serine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Fusarium oxysporum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å | ||||||
Authors | Schmidt, A. / Jelsch, C. / Rypniewski, W. / Lamzin, V.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Trypsin Revisited: CRYSTALLOGRAPHY AT (SUB) ATOMIC RESOLUTION AND QUANTUM CHEMISTRY REVEALING DETAILS OF CATALYSIS. Authors: Schmidt, A. / Jelsch, C. / Ostergaard, P. / Rypniewski, W. / Lamzin, V.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pq8.cif.gz | 146.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pq8.ent.gz | 123 KB | Display | PDB format |
PDBx/mmJSON format | 1pq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pq8_validation.pdf.gz | 479.4 KB | Display | wwPDB validaton report |
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Full document | 1pq8_full_validation.pdf.gz | 488.5 KB | Display | |
Data in XML | 1pq8_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 1pq8_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/1pq8 ftp://data.pdbj.org/pub/pdb/validation_reports/pq/1pq8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AC
#1: Protein | Mass: 22200.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fusarium oxysporum (fungus) / References: UniProt: P35049, trypsin |
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#2: Protein/peptide | Mass: 289.313 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide is chemically synthesized. |
-Non-polymers , 4 types, 332 molecules
#3: Chemical | #4: Chemical | ChemComp-LYS / | #5: Chemical | ChemComp-CIT / | #6: Water | ChemComp-HOH / | |
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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: 1.94 Å3/Da / Density % sol: 36.54 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: Na-sulphate, Na-Citrate, pH 4, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Rypniewski, W.R., (1993) Protein Eng., 6, 341. / PH range low: 5.5 / PH range high: 5 | ||||||||||||||||||||||||||||||
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: EMBL/DESY, Hamburg / Beamline: X13 / Wavelength: 0.802 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.802 Å / Relative weight: 1 |
Reflection | Resolution: 1→25 Å / Num. all: 86840 / Num. obs: 86840 / % possible obs: 94.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 7.1 Å2 / Rsym value: 0.073 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1→1.01 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.385 / % possible all: 92.6 |
Reflection | *PLUS Highest resolution: 1 Å / Lowest resolution: 22 Å / Num. obs: 86663 / Rmerge(I) obs: 0.073 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1→20 Å / Num. parameters: 19056 / Num. restraintsaints: 25644 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT. Initially Rfree (building stage) was used (10% of data at random), later none. There is a peptide chain C, GLY-GLY-ARG. The ARG is in two alternate conformations, A ...Details: ANISOTROPIC REFINEMENT. Initially Rfree (building stage) was used (10% of data at random), later none. There is a peptide chain C, GLY-GLY-ARG. The ARG is in two alternate conformations, A and B. There is a LYS 403 ligand that also occupies the same space as the ARG and is not part of the peptide chain. The LYS is labelled as alternate conformation C.
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Refine analyze | Num. disordered residues: 55 / Occupancy sum hydrogen: 1499.14 / Occupancy sum non hydrogen: 1883.6 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→20 Å
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Software | *PLUS Name: SHELXL / Version: 96 / Classification: refinement | ||||||||||||||||
Refinement | *PLUS Highest resolution: 1 Å / Rfactor Rwork: 0.128 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS |