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Yorodumi- PDB-5dm1: Crystal structure of the plantazolicin methyltransferase BpumL in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dm1 | ||||||
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Title | Crystal structure of the plantazolicin methyltransferase BpumL in complex with monoazolic desmethylPZN analog and SAH | ||||||
Components | Methyltransferase domain family | ||||||
Keywords | transferase/transferase inhibitor / N-methyltransferase / plantazolicin / monoazolic desmethylPZN analog / transferase-transferase inhibitor complex | ||||||
Function / homology | Vaccinia Virus protein VP39 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Chem-5D7 / S-ADENOSYL-L-HOMOCYSTEINE / : Function and homology information | ||||||
Biological species | Bacillus pumilus ATCC 7061 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | ||||||
Authors | Hao, Y. / Nair, S.K. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2015 Title: Insights into methyltransferase specificity and bioactivity of derivatives of the antibiotic plantazolicin. Authors: Hao, Y. / Blair, P.M. / Sharma, A. / Mitchell, D.A. / Nair, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dm1.cif.gz | 69.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dm1.ent.gz | 50.2 KB | Display | PDB format |
PDBx/mmJSON format | 5dm1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dm1_validation.pdf.gz | 934.8 KB | Display | wwPDB validaton report |
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Full document | 5dm1_full_validation.pdf.gz | 935.9 KB | Display | |
Data in XML | 5dm1_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 5dm1_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/5dm1 ftp://data.pdbj.org/pub/pdb/validation_reports/dm/5dm1 | 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: 30573.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus pumilus ATCC 7061 (bacteria) / Gene: BAT_2465 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: B4ADV2 |
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#2: Chemical | ChemComp-5D7 / |
#3: Chemical | ChemComp-SAH / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.79 % |
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Crystal grow | Temperature: 282 K / Method: vapor diffusion, hanging drop Details: 100mM Bis-tris pH 5.5, 200mM Li2SO4, 22-26% PEG3350 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.987 Å |
Detector | Type: RAYONIX MX-325 / Detector: CCD / Date: Aug 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25 Å / Num. obs: 22653 / % possible obs: 99.54 % / Redundancy: 6.6 % / Net I/σ(I): 9.2 |
-Processing
Software |
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Refinement | Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.711 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.965 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→25 Å
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Refine LS restraints |
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