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Yorodumi- PDB-4pwy: Crystal structure of a Calmodulin-lysine N-methyltransferase fragment -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pwy | ||||||
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Title | Crystal structure of a Calmodulin-lysine N-methyltransferase fragment | ||||||
Components | Calmodulin-lysine N-methyltransferase | ||||||
Keywords | TRANSFERASE / structural genomics / methyl transferase / Structural Genomics Consortium / SGC / PSI-Biology | ||||||
Function / homology | Function and homology information calmodulin-lysine N-methyltransferase / calmodulin-lysine N-methyltransferase activity / regulation of opsin-mediated signaling pathway / protein methylation / Protein methylation / heat shock protein binding / mitochondrion organization / Inactivation, recovery and regulation of the phototransduction cascade / Golgi apparatus / protein-containing complex ...calmodulin-lysine N-methyltransferase / calmodulin-lysine N-methyltransferase activity / regulation of opsin-mediated signaling pathway / protein methylation / Protein methylation / heat shock protein binding / mitochondrion organization / Inactivation, recovery and regulation of the phototransduction cascade / Golgi apparatus / protein-containing complex / nucleoplasm / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Tempel, W. / Hong, B.S. / Walker, J.R. / Li, Y. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of a Calmodulin-lysine N-methyltransferase fragment Authors: Tempel, W. / Hong, B.S. / Walker, J.R. / Li, Y. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pwy.cif.gz | 73.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pwy.ent.gz | 52.1 KB | Display | PDB format |
PDBx/mmJSON format | 4pwy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pwy_validation.pdf.gz | 753.8 KB | Display | wwPDB validaton report |
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Full document | 4pwy_full_validation.pdf.gz | 754 KB | Display | |
Data in XML | 4pwy_validation.xml.gz | 13 KB | Display | |
Data in CIF | 4pwy_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/4pwy ftp://data.pdbj.org/pub/pdb/validation_reports/pw/4pwy | HTTPS FTP |
-Related structure data
Related structure data | 3bzbS 4lecS 4lg1S 4mtlS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 30020.076 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CAMKMT, C2orf34, CLNMT / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) V2R-pRARE References: UniProt: Q7Z624, calmodulin-lysine N-methyltransferase |
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-Non-polymers , 5 types, 129 molecules
#2: Chemical | ChemComp-SAH / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-UNX / #5: Chemical | ChemComp-MLI / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6.7 Details: 2.0 M malonate, pH 6.7, vapor diffusion, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 10, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 32722 / % possible obs: 100 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.107 / Χ2: 1.474 / Net I/σ(I): 9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: FFAS03/SCWRL-modified models of PDB entries 4lec, 3bzb, 4lg1, 4mtl Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.1665 / WRfactor Rwork: 0.1432 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.876 / SU B: 2.156 / SU ML: 0.064 / SU R Cruickshank DPI: 0.1004 / SU Rfree: 0.1008 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Arp/Warp was used for map improvement and automated model building. COOT was used for interactive model building. Model geometry was evaluated with MOLPROBITY.
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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: 85.03 Å2 / Biso mean: 22.9872 Å2 / Biso min: 12.06 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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