+Open data
-Basic information
Entry | Database: PDB / ID: 4z2y | ||||||
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Title | Crystal structure of methyltransferase CalO6 | ||||||
Components | CalO6 | ||||||
Keywords | TRANSFERASE / O-methyltransferase / calicheamicin / anticancer / antibiotic | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Micromonospora echinospora (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.4 Å | ||||||
Authors | Hou, C. / Garneau-Tsodikova, S. / Tsodikov, O.V. | ||||||
Citation | Journal: Bmc Struct.Biol. / Year: 2015 Title: Crystal structure of O-methyltransferase CalO6 from the calicheamicin biosynthetic pathway: a case of challenging structure determination at low resolution. Authors: Tsodikov, O.V. / Hou, C. / Walsh, C.T. / Garneau-Tsodikova, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z2y.cif.gz | 127.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z2y.ent.gz | 100.3 KB | Display | PDB format |
PDBx/mmJSON format | 4z2y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/4z2y ftp://data.pdbj.org/pub/pdb/validation_reports/z2/4z2y | HTTPS FTP |
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-Related structure data
Similar structure data |
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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: 38312.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: calO6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8KND2 | ||
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#2: Chemical | #3: 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: 2.13 Å3/Da / Density % sol: 42.37 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: Reservoir: 0.1 M NaCl, 0.1 M Bis-Tris (pH 5.8), and 1.10-1.25 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.007 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 20, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.007 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 11759 / % possible obs: 98.07 % / Redundancy: 3.4 % / Net I/σ(I): 28 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.4→25 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.846 / SU B: 144.519 / SU ML: 1.032 / Cross valid method: THROUGHOUT / ESU R Free: 0.826 / 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: 110.344 Å2
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Refinement step | Cycle: 1 / Resolution: 3.4→25 Å
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Refine LS restraints |
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