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- PDB-6aw8: 2.25A resolution domain swapped dimer structure of SAH bound cate... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6aw8 | ||||||
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Title | 2.25A resolution domain swapped dimer structure of SAH bound catechol O-methyltransferase (COMT) from Nannospalax galili | ||||||
![]() | Catechol O-methyltransferase | ||||||
![]() | TRANSFERASE / Spalax / COMT / S-adenosylmethionine binding | ||||||
Function / homology | ![]() catecholamine catabolic process / catechol O-methyltransferase activity / : / : / catechol O-methyltransferase / developmental process / dopamine metabolic process / methylation / axon / dendrite ...catecholamine catabolic process / catechol O-methyltransferase activity / : / : / catechol O-methyltransferase / developmental process / dopamine metabolic process / methylation / axon / dendrite / magnesium ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Lovell, S. / Mehzabeen, N. / Battaile, K.P. / Deng, Y. / Hanzlik, R.P. / Shams, I. / Moskovitz, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of the catechol-o-methyl transferase (COMT) enzyme of the subterranean mole rat (Spalax) and the effect of L136M substitution Authors: Deng, Y. / Lovell, S. / Mehzabeen, N. / Battaile, K.P. / Hanzlik, R.P. / Shams, I. / Moskovitz, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.1 KB | Display | ![]() |
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PDB format | ![]() | 109.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 25.2 KB | Display | |
Data in CIF | ![]() | 34.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6aw4C ![]() 6aw5C ![]() 6aw6C ![]() 6aw7C ![]() 6aw9C ![]() 2zlbS S: Starting model for refinement C: citing same article ( |
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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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25717.373 Da / Num. of mol.: 3 / Fragment: M43-P262 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pET28a / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.38 % / Mosaicity: 0.09 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 14.4 % (w/v) PEG 8000, 80 mM sodium cacodylate, 160 mM calcium chloride, 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→48.77 Å / Num. obs: 45368 / % possible obs: 97.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 42.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.9 / Num. measured all: 292792 / Scaling rejects: 3 |
Reflection shell | Resolution: 2.25→2.32 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.906 / Num. unique obs: 4104 / CC1/2: 0.774 / % possible all: 98.2 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ZLB Resolution: 2.25→46.197 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.05 / Phase error: 23.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 151.97 Å2 / Biso mean: 50.0581 Å2 / Biso min: 27.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.25→46.197 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16
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