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Yorodumi- PDB-4qvg: Crystal structure of S-adenosylmethionine-dependent methyltransfe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qvg | ||||||
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Title | Crystal structure of S-adenosylmethionine-dependent methyltransferase SibL in its apo form | ||||||
Components | SibL | ||||||
Keywords | TRANSFERASE / methyltransferase | ||||||
Function / homology | Function and homology information acetylserotonin O-methyltransferase activity / melatonin biosynthetic process / S-adenosyl-L-methionine binding / methyltransferase activity / methylation Similarity search - Function | ||||||
Biological species | Streptosporangium sibiricum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Liu, J.S. / Chen, S.C. / Huang, C.H. / Yang, C.S. / Chen, Y. | ||||||
Citation | Journal: Sci Rep / Year: 2015 Title: Structure and mechanism of an antibiotics-synthesizing 3-hydroxykynurenine C-methyltransferase Authors: Chen, S.C. / Huang, C.H. / Lai, S.J. / Liu, J.S. / Fu, P.K. / Tseng, S.T. / Yang, C.S. / Lai, M.C. / Ko, T.P. / Chen, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qvg.cif.gz | 262 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qvg.ent.gz | 215.5 KB | Display | PDB format |
PDBx/mmJSON format | 4qvg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qvg_validation.pdf.gz | 458.2 KB | Display | wwPDB validaton report |
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Full document | 4qvg_full_validation.pdf.gz | 473.9 KB | Display | |
Data in XML | 4qvg_validation.xml.gz | 46 KB | Display | |
Data in CIF | 4qvg_validation.cif.gz | 63.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/4qvg ftp://data.pdbj.org/pub/pdb/validation_reports/qv/4qvg | HTTPS FTP |
-Related structure data
Related structure data | 4u1qS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 38923.797 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptosporangium sibiricum (bacteria) / Gene: sibL / Production host: Escherichia coli (E. coli) / References: UniProt: C0LTM6 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.93 Å3/Da / Density % sol: 68.73 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 10%(v/v) Polyethylene glycol 200, 0.1 M BIS-TRIS propane pH 9.0, 18%(w/v) Polyethylene glycol 8,000 , VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2013 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. all: 54894 / Num. obs: 54730 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.211 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4U1Q Resolution: 2.9→28.116 Å / SU ML: 0.36 / σ(F): 1.34 / Phase error: 29.04 / 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: 2.9→28.116 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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