+Open data
-Basic information
Entry | Database: PDB / ID: 4rvg | ||||||
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Title | Crystal structure of MtmC in complex with SAM and TDP | ||||||
Components | D-mycarose 3-C-methyltransferase | ||||||
Keywords | TRANSFERASE / C-methyltransferase / TDP-4-keto-D-olivose | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces argillaceus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Tsodikov, O.V. / Hou, C. / Chen, J.-M. / Rohr, J. | ||||||
Citation | Journal: Biochemistry / Year: 2015 Title: Structural Insight into MtmC, a Bifunctional Ketoreductase-Methyltransferase Involved in the Assembly of the Mithramycin Trisaccharide Chain. Authors: Chen, J.M. / Hou, C. / Wang, G. / Tsodikov, O.V. / Rohr, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rvg.cif.gz | 99.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rvg.ent.gz | 74.2 KB | Display | PDB format |
PDBx/mmJSON format | 4rvg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/4rvg ftp://data.pdbj.org/pub/pdb/validation_reports/rv/4rvg | HTTPS FTP |
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-Related structure data
-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 46925.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces argillaceus (bacteria) / Gene: mtmC / Production host: Escherichia coli (E. coli) / References: UniProt: Q194Q4 |
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-Non-polymers , 5 types, 154 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-TYD / |
#4: Chemical | ChemComp-SAM / |
#5: Chemical | ChemComp-ACT / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.18 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M MES, pH 5.5, 0.2 M ammonium acetate, 16% PEG 4000, 1 mM TDP, 1 mM SAM, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 29, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40 Å / Num. obs: 24771 / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.08 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.209 / 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: 45.663 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→40 Å
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Refine LS restraints |
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