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Yorodumi- PDB-3i5u: Crystal structure of an O-methyltransferase (NcsB1) from neocarzi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i5u | ||||||
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Title | Crystal structure of an O-methyltransferase (NcsB1) from neocarzinostatin biosynthesis in complex with S-adenosylmethionine (SAM) and 2-hydroxy-5-methyl naphthoic acid (MNA) | ||||||
Components | O-methyltransferase | ||||||
Keywords | TRANSFERASE / co-complex / Rossmann-like fold / Methyltransferase | ||||||
Function / homology | Function and homology information 2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / O-methyltransferase activity / antibiotic biosynthetic process / methylation Similarity search - Function | ||||||
Biological species | Streptomyces carzinostaticus subsp. neocarzinostaticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Cooke, H.A. / Bruner, S.D. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Molecular basis of substrate promiscuity for the SAM-dependent O-methyltransferase NcsB1, involved in the biosynthesis of the enediyne antitumor antibiotic neocarzinostatin. Authors: Cooke, H.A. / Guenther, E.L. / Luo, Y. / Shen, B. / Bruner, S.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i5u.cif.gz | 136.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i5u.ent.gz | 106.7 KB | Display | PDB format |
PDBx/mmJSON format | 3i5u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/3i5u ftp://data.pdbj.org/pub/pdb/validation_reports/i5/3i5u | HTTPS FTP |
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-Related structure data
Related structure data | 3i53C 3i58C 3i64C 1tw2S C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 34633.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces carzinostaticus subsp. neocarzinostaticus (bacteria) Gene: ncsb1 / Plasmid: pBS5002 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q84HC8, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 5.13 Å3/Da / Density % sol: 76.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.8 Details: 3.6 M Sodium formate, 10% Glycerol, 2 mM SAM, 2 mM MNA, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 14, 2008 |
Radiation | Monochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 42568 / % possible obs: 99.8 % / Redundancy: 22.7 % / Biso Wilson estimate: 49.7 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 49.6 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 22.9 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 6.4 / Num. unique all: 4243 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1TW2 Resolution: 2.6→30.13 Å / Cross valid method: FREE R
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Displacement parameters | Biso mean: 55.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→30.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
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