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Yorodumi- PDB-4bp9: Oligopeptidase B from Trypanosoma brucei with covalently bound an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bp9 | ||||||||||||
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Title | Oligopeptidase B from Trypanosoma brucei with covalently bound antipain - closed form | ||||||||||||
Components |
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Keywords | HYDROLASE / PROLYL OLIGOPEPTIDASE | ||||||||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / serine-type endopeptidase activity / proteolysis / cytoplasm Similarity search - Function | ||||||||||||
Biological species | TRYPANOSOMA BRUCEI (eukaryote) ACTINOBACTERIA (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||||||||
Authors | Canning, P. / Rea, D. / Morty, R. / Fulop, V. | ||||||||||||
Citation | Journal: Plos One / Year: 2013 Title: Crystal Structures of Trypanosoma Brucei Oligopeptidase B Broaden the Paradigm of Catalytic Regulation in Prolyl Oligopeptidase Family Enzymes. Authors: Canning, P. / Rea, D. / Morty, R.E. / Fulop, V. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bp9.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4bp9.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 4bp9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/4bp9 ftp://data.pdbj.org/pub/pdb/validation_reports/bp/4bp9 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 80790.688 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PRARE / References: UniProt: O76728, EC: 3.4.21.83 #2: Protein/peptide | #3: Water | ChemComp-HOH / | Compound details | ANTIPAIN HYDROCHLORIDE IS A REVERSIBLE INHIBITOR OF SERINE/CYSTEINE PROTEASES AND SOME TRYPSIN-LIKE ...ANTIPAIN HYDROCHLOR | Nonpolymer details | ANTIPAIN: COVALENTLY | |
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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: 3 Å3/Da / Density % sol: 59 % Description: STARTING MODEL IS ALSO BEING CURRENTLY DEPOSITED |
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Crystal grow | pH: 5 Details: 10 % PEG 4000, 0.2 M CALCIUM ACETATE, 0.1 M SODIUM ACETATE PH 5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9778 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 27, 2009 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→59 Å / Num. obs: 127053 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 45.4 Å2 / Rmerge(I) obs: 0.22 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.85→3 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 2.2 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→58.59 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.882 / SU B: 43.636 / SU ML: 0.381 / Cross valid method: THROUGHOUT / ESU R Free: 0.436 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 59.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→58.59 Å
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