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Yorodumi- PDB-8ono: Modified oligopeptidase B from S. proteamaculans in intermediate ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ono | ||||||
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Title | Modified oligopeptidase B from S. proteamaculans in intermediate conformation with 5 spermine molecule at 1.65 A resolution | ||||||
Components | Oligopeptidase B | ||||||
Keywords | HYDROLASE / protease | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Serratia proteamaculans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Petrenko, D.E. / Boyko, K.M. / Nikolaeva, A.Y. / Vlaskina, A.V. / Mikhailova, A.G. / Timofeev, V.I. / Rakitina, T.V. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Modified oligopeptidase B from S. proteomaculans in intermediate conformation with 5 spermine molecule at 1.65 A resolution Authors: Petrenko, D.E. / Boyko, K.M. / Nikolaeva, A.Y. / Vlaskina, A.V. / Mikhailova, A.G. / Timofeev, V.I. / Rakitina, T.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ono.cif.gz | 160.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ono.ent.gz | 126.5 KB | Display | PDB format |
PDBx/mmJSON format | 8ono.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/8ono ftp://data.pdbj.org/pub/pdb/validation_reports/on/8ono | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 78459.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia proteamaculans (bacteria) / Gene: opdB / Production host: Serratia proteamaculans (bacteria) / References: UniProt: B3VI58 | ||||
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#2: Chemical | ChemComp-SPM / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.68 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 200 mM Lithium sulfate, 100 mM Bis-Tris pH 5.5, 23% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30 Å / Num. obs: 95311 / % possible obs: 98.57 % / Redundancy: 5.84 % / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.056 / Net I/σ(I): 9.2633 |
Reflection shell | Resolution: 1.65→1.74 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.29 / Num. unique obs: 13658 / Rrim(I) all: 0.359 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→29.59 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.806 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.035 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→29.59 Å
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Refine LS restraints |
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