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Yorodumi- PDB-2xdw: Inhibition of Prolyl Oligopeptidase with a Synthetic Unnatural Di... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xdw | ||||||
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Title | Inhibition of Prolyl Oligopeptidase with a Synthetic Unnatural Dipeptide | ||||||
Components |
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Keywords | HYDROLASE / ALPHA/BETA-HYDROLASE / AMNESIA / BETA-PROPELLER / INHIBITOR | ||||||
Function / homology | Function and homology information prolyl oligopeptidase / oligopeptidase activity / serine-type endopeptidase activity / proteolysis / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | SUS SCROFA (pig) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Racys, D.T. / Rea, D. / Fulop, V. / Wills, M. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2010 Title: Inhibition of Prolyl Oligopeptidase with a Synthetic Unnatural Dipeptide Authors: Racys, D.T. / Rea, D. / Fulop, V. / Wills, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xdw.cif.gz | 307.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xdw.ent.gz | 247.7 KB | Display | PDB format |
PDBx/mmJSON format | 2xdw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xdw_validation.pdf.gz | 463.5 KB | Display | wwPDB validaton report |
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Full document | 2xdw_full_validation.pdf.gz | 467.8 KB | Display | |
Data in XML | 2xdw_validation.xml.gz | 37.8 KB | Display | |
Data in CIF | 2xdw_validation.cif.gz | 60.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xd/2xdw ftp://data.pdbj.org/pub/pdb/validation_reports/xd/2xdw | HTTPS FTP |
-Related structure data
Related structure data | 1qfsS S: Starting model for refinement |
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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: 80864.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SUS SCROFA (pig) / Organ: BRAIN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM105 / References: UniProt: P23687, prolyl oligopeptidase | ||
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#2: Protein/peptide | Mass: 378.850 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) | ||
#3: Chemical | ChemComp-TAM / | ||
#4: Chemical | ChemComp-GOL / #5: 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: 2.5 Å3/Da / Density % sol: 44 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 18-20% METHOXY-POLYETHYLENE GLYCOL (MPEG) 5K, 20 MM CA(OAC)2, 0.1 M TRIS PH=8.5, 15% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9702 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 9, 2009 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9702 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→51.2 Å / Num. obs: 168431 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.35→1.42 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.1 / % possible all: 99.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QFS Resolution: 1.35→51.31 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.675 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→51.31 Å
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Refine LS restraints |
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