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Open data
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Basic information
Entry | Database: PDB / ID: 2wk1 | ||||||
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Title | Structure of the O-methyltransferase NovP | ||||||
![]() | NOVP | ||||||
![]() | TRANSFERASE / NOVP / O-METHYLTRANSFERASE / NOVOBIOCIN / TYLF SUPERFAMILY | ||||||
Function / homology | ![]() demethyldecarbamoylnovobiocin O-methyltransferase / novobiocin biosynthetic process / methyltransferase activity / methylation / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gomez Garcia, I. / Stevenson, C.E.M. / Uson, I. / Freel Meyers, C.L. / Walsh, C.T. / Lawson, D.M. | ||||||
![]() | ![]() Title: The Crystal Structure of the Novobiocin Biosynthetic Enzyme Novp: The First Representative Structure for the Tylf O-Methyltransferase Superfamily. Authors: Gomez Garcia, I. / Stevenson, C.E.M. / Uson, I. / Freel Meyers, C.L. / Walsh, C.T. / Lawson, D.M. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2007 Title: Crystallization and Preliminary X-Ray Analysis of the O-Methyltransferase Novp from the Novobiocin-Biosynthetic Cluster of Streptomyces Spheroides. Authors: Stevenson, C.E.M. / Freel Meyers, C.L. / Walsh, C.T. / Lawson, D.M. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: Structure Determination of the O-Methyltransferase Novp Using the 'Free Lunch Algorithm' as Implemented in Shelxe. Authors: Uson, I. / Stevenson, C.E.M. / Lawson, D.M. / Sheldrick, G.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125.8 KB | Display | ![]() |
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PDB format | ![]() | 95.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 715.5 KB | Display | ![]() |
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Full document | ![]() | 721.6 KB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 22.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1vidS 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 on special symmetry positions |
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Components
#1: Protein | Mass: 32175.088 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: DISULPHIDE BRIDGE BETWEEN CYS228 AND CYS231 / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9L9F2, Transferases; Transferring one-carbon groups; Methyltransferases | ||||
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#2: Chemical | ChemComp-SAH / | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.9 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 2 M AMMONIUM SULPHATE, 100 MM HEPES BUFFER PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 14, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→36.3 Å / Num. obs: 54638 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.4→1.42 Å / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 4.2 / % possible all: 89.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1VID Resolution: 1.4→34.1 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.321 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DATA WERE COLLECTED TO A MAXIMUM RESOLUTION OF 1.35 ANGSTROM, BUT WERE NOT VERY COMPLETE IN THE OUTER RESOLUTION SHELL, SO ONLY THE DATA TO ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DATA WERE COLLECTED TO A MAXIMUM RESOLUTION OF 1.35 ANGSTROM, BUT WERE NOT VERY COMPLETE IN THE OUTER RESOLUTION SHELL, SO ONLY THE DATA TO 1.4 ANGSTROM RESOLUTION WERE USED FOR THE REFINEMENT. HOWEVER, THE STRUCTURE WAS SOLVED USING ALL AVAILABLE NATIVE DATA INCLUDING THREE OTHER NATIVE DATA SETS COLLECTED AT LOWER RESOLUTIONS. THIS MERGED NATIVE DATA SET HAS ALSO BEEN DEPOSITED. SEE REFERENCE 2 (USON ET AL., 2007) FOR FURTHER DETAILS.
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Solvent computation | Ion probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.38 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→34.1 Å
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Refine LS restraints |
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