+Open data
-Basic information
Entry | Database: PDB / ID: 5zy6 | ||||||
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Title | catechol methyltransferase spCOMT | ||||||
Components | Probable catechol O-methyltransferase 1 | ||||||
Keywords | TRANSFERASE / catechol / methyltransferase | ||||||
Function / homology | Function and homology information Enzymatic degradation of dopamine by COMT / catechol O-methyltransferase / catecholamine metabolic process / O-methyltransferase activity / methylation / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe 972h- (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å | ||||||
Authors | Wang, Q. / Xu, L. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: structural insight into spCOMT Authors: Wang, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zy6.cif.gz | 220 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zy6.ent.gz | 173.7 KB | Display | PDB format |
PDBx/mmJSON format | 5zy6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zy6_validation.pdf.gz | 922 KB | Display | wwPDB validaton report |
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Full document | 5zy6_full_validation.pdf.gz | 923.5 KB | Display | |
Data in XML | 5zy6_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 5zy6_validation.cif.gz | 32.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/5zy6 ftp://data.pdbj.org/pub/pdb/validation_reports/zy/5zy6 | HTTPS FTP |
-Related structure data
Related structure data | 4pyjS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31413.025 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast) Strain: 972 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: O42898, catechol O-methyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.49 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 21% PEG4000, 0.1% MES pH5.6, (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Nov 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.099→50 Å / Num. obs: 34385 / % possible obs: 99.4 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 35 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 9 / Num. unique obs: 1668 / Rsym value: 0.253 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4pyj Resolution: 2.099→36.813 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 23.43
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.099→36.813 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -24.5584 Å / Origin y: 9.2522 Å / Origin z: -6.8336 Å
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Refinement TLS group | Selection details: all |