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Yorodumi- PDB-4kwc: Structure of the plantazolicin methyltransferase BpumL in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kwc | ||||||
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Title | Structure of the plantazolicin methyltransferase BpumL in complex with SAH | ||||||
Components | BpumL | ||||||
Keywords | TRANSFERASE / TOMM / methyltransferase | ||||||
Function / homology | Vaccinia Virus protein VP39 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / S-ADENOSYL-L-HOMOCYSTEINE / : Function and homology information | ||||||
Biological species | Bacillus pumilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.994 Å | ||||||
Authors | Hao, Y. / Nair, S.K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Structural and functional insight into an unexpectedly selective N-methyltransferase involved in plantazolicin biosynthesis. Authors: Lee, J. / Hao, Y. / Blair, P.M. / Melby, J.O. / Agarwal, V. / Burkhart, B.J. / Nair, S.K. / Mitchell, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kwc.cif.gz | 70.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kwc.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 4kwc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kwc_validation.pdf.gz | 722.4 KB | Display | wwPDB validaton report |
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Full document | 4kwc_full_validation.pdf.gz | 724.3 KB | Display | |
Data in XML | 4kwc_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 4kwc_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/4kwc ftp://data.pdbj.org/pub/pdb/validation_reports/kw/4kwc | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 33427.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus pumilus (bacteria) / Gene: BAT_2465 / Production host: Escherichia coli (E. coli) References: UniProt: B4ADV2, Transferases; Transferring one-carbon groups; Methyltransferases |
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#2: Chemical | ChemComp-SAH / |
#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: 1.76 Å3/Da / Density % sol: 29.98 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å |
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Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Monochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.994→50 Å / Num. obs: 15809 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.994→2.07 Å / % possible all: 68.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.994→38.879 Å / SU ML: 0.24 / σ(F): 1.35 / Phase error: 26.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.994→38.879 Å
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Refine LS restraints |
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LS refinement shell |
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