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Yorodumi- PDB-5dm0: Crystal structure of the plantazolicin methyltransferase BamL in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dm0 | ||||||
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Title | Crystal structure of the plantazolicin methyltransferase BamL in complex with triazolic desmethylPZN analog and SAH | ||||||
Components | plantazolicin methyltransferase BamL | ||||||
Keywords | transferase/transferase inhibitor / N-methyltransferase / plantazolicin / desmethylPZN analog / transferase-transferase inhibitor complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus amyloliquefaciens subsp. plantarum | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 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 | 5dm0.cif.gz | 133.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dm0.ent.gz | 103.8 KB | Display | PDB format |
PDBx/mmJSON format | 5dm0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/5dm0 ftp://data.pdbj.org/pub/pdb/validation_reports/dm/5dm0 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 30966.955 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus amyloliquefaciens subsp. plantarum (strain DSM 23117 / BGSC 10A6 / FZB42) (bacteria) Strain: DSM 23117 / BGSC 10A6 / FZB42 / Gene: RBAM_007500 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: A7Z2A9 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.68 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 100mM Bis-tris, 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-225 / 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: 1.75→25 Å / Num. obs: 64060 / % possible obs: 99.48 % / Redundancy: 6.9 % / Net I/σ(I): 6.2 |
-Processing
Software |
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Refinement | Resolution: 1.75→25 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.142 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.108 / 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: 22.276 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→25 Å
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Refine LS restraints |
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