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- PDB-7cvw: Crystal structure of Catechol o-methyl transferase (COMT) from Ni... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7cvw | ||||||
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Title | Crystal structure of Catechol o-methyl transferase (COMT) from Niastella koreensis | ||||||
![]() | O-methyltransferase family 3 | ||||||
![]() | TRANSFERASE / Catechol o-methyl transferase / Mannheimia succiniciproducens / succinate production / TCA cycle / LYASE | ||||||
Function / homology | ![]() catechol O-methyltransferase / S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / methylation / metal ion binding Similarity search - Function | ||||||
Biological species | Niastella koreensis | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, B. / Lee, S.H. / Kim, K.-J. | ||||||
![]() | ![]() Title: Structural and Biochemical analysis of FumaraseC from Mannheimia succiniciproducens Authors: Kim, B. / Lee, S.H. / Kim, K.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 | ![]() | 101.9 KB | Display | ![]() |
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PDB format | ![]() | 74.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 18.6 KB | Display | |
Data in CIF | ![]() | 26.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7c1aC ![]() 7c1cC ![]() 7cvuC ![]() 7cvvC ![]() 7cvxC ![]() 5n5dS 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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Unit cell |
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Components
#1: Protein | Mass: 25128.637 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 17620 / KACC 11465 / NBRC 106392 / GR20-10 / Gene: Niako_0425 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.06 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 20% PEG4000, 20% 2-Propanol and 0.1M Sodium citrate pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 16, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.54→50 Å / Num. obs: 63757 / % possible obs: 99.5 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.035 / Rrim(I) all: 0.092 / Χ2: 2.526 / Net I/σ(I): 12.3 / Num. measured all: 394759 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5N5D Resolution: 1.54→27.55 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.296 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 55.87 Å2 / Biso mean: 13.533 Å2 / Biso min: 2.5 Å2
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Refinement step | Cycle: final / Resolution: 1.54→27.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.541→1.581 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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