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Yorodumi- PDB-7sfp: Crystal structure of OssO, a spirocyclase involved in the biosynt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sfp | |||||||||
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Title | Crystal structure of OssO, a spirocyclase involved in the biosynthesis of ossamycin | |||||||||
Components | Spirocyclase | |||||||||
Keywords | HYDROLASE / cyclase / spyrocyclase / oligomycin / calycin | |||||||||
Function / homology | Putative spirocyclase Function and homology information | |||||||||
Biological species | Streptomyces ossamyceticus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Bilyk, O. / Leadlay, P.F. / Dias, M.V.B. | |||||||||
Funding support | Brazil, 2items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2022 Title: Enzyme-Catalyzed Spiroacetal Formation in Polyketide Antibiotic Biosynthesis. Authors: Bilyk, O. / Oliveira, G.S. / de Angelo, R.M. / Almeida, M.O. / Honorio, K.M. / Leeper, F.J. / Dias, M.V.B. / Leadlay, P.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sfp.cif.gz | 79.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sfp.ent.gz | 57.7 KB | Display | PDB format |
PDBx/mmJSON format | 7sfp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sfp_validation.pdf.gz | 433.8 KB | Display | wwPDB validaton report |
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Full document | 7sfp_full_validation.pdf.gz | 433.9 KB | Display | |
Data in XML | 7sfp_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 7sfp_validation.cif.gz | 9.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sf/7sfp ftp://data.pdbj.org/pub/pdb/validation_reports/sf/7sfp | HTTPS FTP |
-Related structure data
Related structure data | 7sfnSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 23832.330 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces ossamyceticus (bacteria) / Gene: ossO Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A481S8L7 |
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#2: 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: 2.16 Å3/Da / Density % sol: 43.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 20 %w/v PEG 8K, 0.1 M 0.2 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 R 100K-A / Detector: PIXEL / Date: Mar 25, 2017 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.2→49.02 Å / Num. obs: 11716 / % possible obs: 100 % / Redundancy: 50 % / CC1/2: 1 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.018 / Rrim(I) all: 0.124 / Net I/σ(I): 25 / Num. measured all: 586280 / Scaling rejects: 1 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 99.9
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7SFN Resolution: 2.2→46.725 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 133.38 Å2 / Biso mean: 68.077 Å2 / Biso min: 40.8 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→46.725 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 37.977 Å / Origin y: 88.3981 Å / Origin z: 256.9182 Å
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Refinement TLS group |
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