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- PDB-4ine: Crystal structure of N-methyl transferase (PMT-2) from Caenorhabd... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ine | ||||||
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Title | Crystal structure of N-methyl transferase (PMT-2) from Caenorhabditis elegant complexed with S-adenosyl homocysteine and phosphoethanolamine | ||||||
![]() | Protein PMT-2 | ||||||
![]() | TRANSFERASE / methyl transferase | ||||||
Function / homology | ![]() phosphatidyl-N-methylethanolamine N-methyltransferase activity / : / Neutrophil degranulation / phosphatidylcholine biosynthetic process / methyltransferase activity / methylation Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lukk, T. / Nair, S.K. | ||||||
![]() | ![]() Title: Crystal structure of N-methyl transferase (PMT-2) from Caenorhabditis elegant complexed with S-adenosyl homocysteine and phosphoethanolamine Authors: Lukk, T. / Nair, S.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 212.8 KB | Display | ![]() |
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PDB format | ![]() | 165.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 985.1 KB | Display | ![]() |
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Full document | ![]() | 997.7 KB | Display | |
Data in XML | ![]() | 43.2 KB | Display | |
Data in CIF | ![]() | 67.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ujbS 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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Unit cell |
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Components
#1: Protein | Mass: 51710.957 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE SPECIFIC CLONE IS AN ISOFORM OF THE SEQUENCE OF UNP ENTRY Q22993. RESIDUES LYS 89 AND ASN 93 ...THE SPECIFIC CLONE IS AN ISOFORM OF THE SEQUENCE OF UNP ENTRY Q22993. RESIDUES LYS 89 AND ASN 93 ARE LINKED TOGETHER | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.8 % |
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Crystal grow | Temperature: 282 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein solution was at 15 mg/mL containing 20 mM Tris (pH 7.5), 100 mM NaCl, 10 mM EDTA and 10 mM bME, 5 mM SAH, 5 mM phosphoethanolamine. Mother liqueur contained 0.04 M potassium ...Details: Protein solution was at 15 mg/mL containing 20 mM Tris (pH 7.5), 100 mM NaCl, 10 mM EDTA and 10 mM bME, 5 mM SAH, 5 mM phosphoethanolamine. Mother liqueur contained 0.04 M potassium phosphate (monobasic), 16% PEG 8,000 and 20% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 282K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jun 3, 2012 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→30 Å / Num. obs: 172409 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rsym value: 0.05 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.634 / % possible all: 93.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 3UJB Resolution: 1.45→29.63 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / Occupancy max: 1 / Occupancy min: 0.38 / SU B: 1.059 / SU ML: 0.041 / SU R Cruickshank DPI: 0.0713 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN
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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: 20.18 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→29.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.49 Å / Total num. of bins used: 20
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