+Open data
-Basic information
Entry | Database: PDB / ID: 4mtl | ||||||
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Title | Human Methyltransferase-Like Protein 21C | ||||||
Components | Protein-lysine methyltransferase METTL21C | ||||||
Keywords | TRANSFERASE / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information peptidyl-lysine methylation / hormone-mediated apoptotic signaling pathway / protein methylation / protein-lysine N-methyltransferase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / skeletal muscle tissue development / heat shock protein binding / cellular response to dexamethasone stimulus / Transferases; Transferring one-carbon groups; Methyltransferases / protein-containing complex ...peptidyl-lysine methylation / hormone-mediated apoptotic signaling pathway / protein methylation / protein-lysine N-methyltransferase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / skeletal muscle tissue development / heat shock protein binding / cellular response to dexamethasone stimulus / Transferases; Transferring one-carbon groups; Methyltransferases / protein-containing complex / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å | ||||||
Authors | Hong, B.S. / Tempel, W. / Dong, A. / Li, Y. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Brown, P.J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Human Methyltransferase-Like Protein 21C Authors: Hong, B.S. / Tempel, W. / Dong, A. / Li, Y. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Brown, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mtl.cif.gz | 193.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mtl.ent.gz | 153.3 KB | Display | PDB format |
PDBx/mmJSON format | 4mtl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mtl_validation.pdf.gz | 962 KB | Display | wwPDB validaton report |
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Full document | 4mtl_full_validation.pdf.gz | 962.6 KB | Display | |
Data in XML | 4mtl_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 4mtl_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/4mtl ftp://data.pdbj.org/pub/pdb/validation_reports/mt/4mtl | HTTPS FTP |
-Related structure data
Related structure data | 4lecS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27490.059 Da / Num. of mol.: 2 / Fragment: UNP residues 22-264 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METTL21C, C13orf39 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) V2R-pRARE References: UniProt: Q5VZV1, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | #3: Chemical | ChemComp-UNX / #4: 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: 2.4 Å3/Da / Density % sol: 48.78 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.5 Details: 30% PEG3350, 0.2 M sodium chloride, 0.1 M HEPES, 0.005 M SAH, pH 7.5, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97856 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2013 |
Radiation | Monochromator: Rosenbaum-Rock high-resolution double-crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→42.09 Å / Num. obs: 62809 / % possible obs: 99.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.097 / Mean I/σ(I) obs: 1.2 / Num. measured all: 11457 / Num. unique all: 3048 / % possible all: 98.1 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4LEC Resolution: 1.65→40.64 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.1891 / WRfactor Rwork: 0.1634 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8542 / SU B: 4.051 / SU ML: 0.072 / SU R Cruickshank DPI: 0.0819 / SU Rfree: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: THE AMINO ACID SEQUENCE OF THE MOLECULAR REPLACEMENT MODEL WAS MODIFIED WITH CHAINSAW. AFTER MOLECULAR REPLACEMENT, PHASES WERE IMPROVED WITH ARP/WARP IN ATOM UPDATE MODE AND WITH DENSITY ...Details: THE AMINO ACID SEQUENCE OF THE MOLECULAR REPLACEMENT MODEL WAS MODIFIED WITH CHAINSAW. AFTER MOLECULAR REPLACEMENT, PHASES WERE IMPROVED WITH ARP/WARP IN ATOM UPDATE MODE AND WITH DENSITY MODIFICATION BY PARROT. AUTOMATIC MODEL BUILDING WAS PERFORMED WITH BUCCANEER, INTERACTIVE MODEL BUILDING WITH COOT, AND GEOMETRY VALIDATION ON THE MOLPROBITY SERVER.
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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: 85.85 Å2 / Biso mean: 34.4981 Å2 / Biso min: 10.76 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→40.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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