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Yorodumi- PDB-4kif: Crystal structure of methyltransferase from Streptomyces hygrosco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kif | |||||||||
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Title | Crystal structure of methyltransferase from Streptomyces hygroscopicus complexed with phenylpyruvic acid | |||||||||
Components | Methyltransferase MppJ | |||||||||
Keywords | TRANSFERASE / Rossmann Fold / Methyltransferase / SAM Binding PPY Binding | |||||||||
Function / homology | Function and homology information phenylpyruvate C3-methyltransferase / antibiotic biosynthetic process / methyltransferase activity / methylation Similarity search - Function | |||||||||
Biological species | Streptomyces hygroscopicus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Liu, Y.C. / Zou, X.W. / Chan, H.C. / Huang, C.J. / Li, T.L. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structure and mechanism of a nonhaem-iron SAM-dependent C-methyltransferase and its engineering to a hydratase and an O-methyltransferase Authors: Zou, X.W. / Liu, Y.C. / Hsu, N.S. / Huang, C.J. / Lyu, S.Y. / Chan, H.C. / Chang, C.Y. / Yeh, H.W. / Lin, K.H. / Wu, C.J. / Tsai, M.D. / Li, T.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kif.cif.gz | 156.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kif.ent.gz | 120.7 KB | Display | PDB format |
PDBx/mmJSON format | 4kif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/4kif ftp://data.pdbj.org/pub/pdb/validation_reports/ki/4kif | HTTPS FTP |
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-Related structure data
Related structure data | 4kibSC 4kicC 4kigC 4m6xC 4m6yC 4m71C 4m72C 4m73C 4m74C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39400.289 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces hygroscopicus (bacteria) / Gene: mppJ / Production host: Escherichia coli (E. coli) / References: UniProt: Q643C8 |
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-Non-polymers , 5 types, 358 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
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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: 2.21 Å3/Da / Density % sol: 44.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 16% PEG3350, 0.2M sodium iodide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jan 21, 2013 |
Radiation | Monochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 23457 / Num. obs: 23457 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.5→2.59 Å / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4KIB Resolution: 2.5→29.43 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.901 / SU B: 9.703 / SU ML: 0.217 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 1.138 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.437 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→29.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.563 Å / Total num. of bins used: 20
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