[English] 日本語
Yorodumi- PDB-3i64: Crystal structure of an O-methyltransferase (NcsB1) from neocarzi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i64 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of an O-methyltransferase (NcsB1) from neocarzinostatin biosynthesis in complex with S-adenosyl-L-homocysteine (SAH) and 1,4-dihydroxy-2-naphthoic acid (DHN) | ||||||
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: 3 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3i64.cif.gz | 134.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3i64.ent.gz | 105.5 KB | Display | PDB format |
PDBx/mmJSON format | 3i64.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3i64_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3i64_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3i64_validation.xml.gz | 29.1 KB | Display | |
Data in CIF | 3i64_validation.cif.gz | 39.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/3i64 ftp://data.pdbj.org/pub/pdb/validation_reports/i6/3i64 | HTTPS FTP |
-Related structure data
Related structure data | 3i53C 3i58C 3i5uC 1tw2S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 5.15 Å3/Da / Density % sol: 76.13 % |
---|---|
Crystal grow | Temperature: 293 K / pH: 3.8 Details: 3.9 M Sodium formate, 10% Glycerol, 2 mM SAH, 2 mM DHN, 10 mM beta-Mercaptoethanol, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 |
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: 2.98→50 Å / Num. obs: 28394 / % possible obs: 99.8 % / Redundancy: 12.6 % / Biso Wilson estimate: 80.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 29.2 |
Reflection shell | Resolution: 2.98→3.09 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 4.2 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TW2 Resolution: 3→50 Å / Cross valid method: FREE R
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.1 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
|