+Open data
-Basic information
Entry | Database: PDB / ID: 6isl | ||||||
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Title | SnoaL-like cyclase XimE with its product xiamenmycin B | ||||||
Components | XimE, SnoaL-like domain protein | ||||||
Keywords | LYASE / SnoaL-like cyslase XimE | ||||||
Function / homology | SnoaL-like domain / SnoaL-like domain / NTF2-like domain superfamily / Chem-XIA / XimE Function and homology information | ||||||
Biological species | Streptomyces xiamenensis 318 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 Å | ||||||
Authors | He, B. / Zhou, T. / Bu, X. / Weng, J. / Xu, J. / Lin, S. / Zheng, J. / Zhao, Y. / Xu, M. | ||||||
Funding support | China, 1items
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Citation | Journal: Acs Catalysis / Year: 2019 Title: Enzymatic Pyran Formation Involved in Xiamenmycin Biosynthesis Authors: He, B. / Zhou, T. / Bu, X. / Weng, J. / Xu, J. / Lin, S. / Zheng, J. / Zhao, Y. / Xu, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6isl.cif.gz | 63 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6isl.ent.gz | 45.4 KB | Display | PDB format |
PDBx/mmJSON format | 6isl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6isl_validation.pdf.gz | 920.5 KB | Display | wwPDB validaton report |
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Full document | 6isl_full_validation.pdf.gz | 921.5 KB | Display | |
Data in XML | 6isl_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 6isl_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/6isl ftp://data.pdbj.org/pub/pdb/validation_reports/is/6isl | HTTPS FTP |
-Related 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: 17205.289 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces xiamenensis 318 (bacteria) Gene: ximE / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: U5Q2N8, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.02 Å3/Da / Density % sol: 39.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 2M xiamenmycin B, 0.2M malonic acid, 20% PEG 3350, pH 4.5 PH range: 3.8-5.5 / Temp details: 293 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9778 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→59.1 Å / Num. obs: 24399 / % possible obs: 100 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.77→1.8 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 3.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.77→59.07 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.669 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.113 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.95 Å2 / Biso mean: 21.267 Å2 / Biso min: 7.22 Å2
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Refinement step | Cycle: final / Resolution: 1.77→59.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.77→1.816 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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