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Yorodumi- PDB-5dm4: Crystal structure of the plantazolicin methyltransferase BpumL in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dm4 | ||||||
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Title | Crystal structure of the plantazolicin methyltransferase BpumL in complex with pentazolic desmethylPZN analog and SAH | ||||||
Components | Methyltransferase domain family | ||||||
Keywords | transferase/transferase inhibitor / N-methyltransferase / plantazolicin / pentazolic desmethylPZN analog / transferase-transferase inhibitor complex | ||||||
Function / homology | Vaccinia Virus protein VP39 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Chem-5DA / S-ADENOSYL-L-HOMOCYSTEINE / : Function and homology information | ||||||
Biological species | Bacillus pumilus ATCC 7061 (bacteria) | ||||||
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 | 5dm4.cif.gz | 72.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dm4.ent.gz | 52 KB | Display | PDB format |
PDBx/mmJSON format | 5dm4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dm4_validation.pdf.gz | 920.9 KB | Display | wwPDB validaton report |
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Full document | 5dm4_full_validation.pdf.gz | 923.5 KB | Display | |
Data in XML | 5dm4_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 5dm4_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/5dm4 ftp://data.pdbj.org/pub/pdb/validation_reports/dm/5dm4 | 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: 30385.580 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-SAH / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-5DA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.19 % |
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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-G / Wavelength: 0.987 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 28, 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: 25053 / % possible obs: 99.96 % / Redundancy: 8 % / Net I/σ(I): 10.7 |
-Processing
Software |
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Refinement | Resolution: 1.75→25 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.633 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.136 / 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: 20.6 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→25 Å
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Refine LS restraints |
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