+Open data
-Basic information
Entry | Database: PDB / ID: 1vz3 | ||||||
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Title | PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, T597C MUTANT | ||||||
Components | PROLYL ENDOPEPTIDASE | ||||||
Keywords | HYDROLASE / PROLYL OLIGOPEPTIDASE / AMNESIA / ALPHA/ BETA-HYDROLASE / BETA-PROPELLER / SERINE PROTEASE | ||||||
Function / homology | Function and homology information prolyl oligopeptidase / oligopeptidase activity / serine-type endopeptidase activity / proteolysis / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | SUS SCROFA (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Rea, D. / Fulop, V. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Concerted Structural Changes in the Peptidase and the Propeller Domains of Prolyl Oligopeptidase are Required for Substrate Binding Authors: Szeltner, Z. / Rea, D. / Juhasz, T. / Renner, V. / Fulop, V. / Polgar, L. #1: Journal: J.Biol.Chem. / Year: 2003 Title: Electrostatic Environment at the Active Site of Prolyl Oligopeptidase is Highly Influential During Substrate Binding Authors: Szeltner, Z. / Rea, D. / Renner, V. / Juliano, L. / Fulop, V. / Polgar, L. #2: Journal: J.Biol.Chem. / Year: 2002 Title: Electrostatic Effects and Binding Determinants in the Catalysis of Prolyl Oligopeptidase: Site Specific Mutagenesis at the Oxyanion Binding Site Authors: Szeltner, Z. / Rea, D. / Renner, V. / Fulop, V. / Polgar, L. #3: Journal: J.Biol.Chem. / Year: 2002 Title: Substrate-Dependent Competency of the Catalytic Triad of Prolyl Oligopeptidase Authors: Szeltner, Z. / Rea, D. / Juhasz, T. / Renner, V. / Mucsi, Z. / Orosz, G. / Fulop, V. / Polgar, L. #4: Journal: J.Biol.Chem. / Year: 2001 Title: Structures of Prolyl Oligopeptidase Substrate/ Inhibitor Complexes. Use of Inhibitor Binding for Titration of the Catalytic Histidine Residue Authors: Fulop, V. / Szeltner, Z. / Renner, V. / Polgar, L. #5: Journal: Embo Rep. / Year: 2000 Title: Catalysis of Serine Oligopeptidases is Controlled by a Gating Filter Mechanism Authors: Fulop, V. / Szeltner, Z. / Polgar, L. #6: Journal: Cell(Cambridge,Mass.) / Year: 1998 Title: Prolyl Oligopeptidase: An Unusual Beta-Propeller Domain Regulates Proteolysis Authors: Fulop, V. / Bocskei, Z. / Polgar, L. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vz3.cif.gz | 181.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vz3.ent.gz | 141.3 KB | Display | PDB format |
PDBx/mmJSON format | 1vz3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/1vz3 ftp://data.pdbj.org/pub/pdb/validation_reports/vz/1vz3 | HTTPS FTP |
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-Related structure data
Related structure data | 1vz2C 1h2wS 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: 80866.383 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: ENGINEERED MUTATION THR 597 CYS / Source: (gene. exp.) SUS SCROFA (pig) / Tissue: BRAIN / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P23687, prolyl oligopeptidase | ||||
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#2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED MUTATION IN CHAIN A, THR 597 CYS IN CHAIN A CLEAVES PEPTIDE BONDS ON THE C-TERMINAL SIDE ...ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 44 % |
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Crystal grow | pH: 8.5 / Details: SEE REMARK 1, REFERENCE 6, pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 10, 2003 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→26 Å / Num. obs: 105437 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 3.2 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H2W Resolution: 1.6→26 Å / SU B: 2.7 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.08
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Displacement parameters | Biso mean: 21.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→26 Å
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