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- PDB-3i58: Crystal structure of an O-methyltransferase (NcsB1) from neocarzi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3i58 | ||||||
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Title | Crystal structure of an O-methyltransferase (NcsB1) from neocarzinostatin biosynthesis in complex with S-adenosyl-L-homocysteine (SAH) and 2-hydroxy-7-methoxy-5-methyl naphthoic acid (NA) | ||||||
![]() | O-methyltransferase | ||||||
![]() | TRANSFERASE / ternary complex / Rossmann-like fold / Methyltransferase | ||||||
Function / homology | ![]() 2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / O-methyltransferase activity / antibiotic biosynthetic process / methylation Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cooke, H.A. / Bruner, S.D. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 136 KB | Display | ![]() |
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PDB format | ![]() | 106.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 28.1 KB | Display | |
Data in CIF | ![]() | 38.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3i53C ![]() 3i5uC ![]() 3i64C ![]() 1tw2S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() Gene: ncsb1 / Plasmid: pBS5002 / Production host: ![]() ![]() 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.15 Å3/Da / Density % sol: 76.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 3.66 M Sodium formate, 10% Glycerol, 2 mM SAH, 2 mM NA, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 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: 2.69→30 Å / Num. obs: 38115 / % possible obs: 98.5 % / Redundancy: 17.3 % / Biso Wilson estimate: 70.7 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2.69→2.8 Å / Redundancy: 17.8 % / Rmerge(I) obs: 0.094 / Mean I/σ(I) obs: 7 / Num. unique all: 3866 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1TW2 Resolution: 2.69→30 Å
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Displacement parameters | Biso mean: 71.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.69→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.69→2.86 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
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