+Open data
-Basic information
Entry | Database: PDB / ID: 6dub | ||||||
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Title | Crystal structure of a methyltransferase | ||||||
Components |
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Keywords | TRANSFERASE / methyltransferase / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information protein N-terminal monomethyltransferase / N-terminal protein amino acid methylation / N-terminal protein N-methyltransferase activity / mitotic nuclear membrane reassembly / sulfate binding / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / Postmitotic nuclear pore complex (NPC) reformation / regulation of mitotic nuclear division / condensed nuclear chromosome ...protein N-terminal monomethyltransferase / N-terminal protein amino acid methylation / N-terminal protein N-methyltransferase activity / mitotic nuclear membrane reassembly / sulfate binding / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / Postmitotic nuclear pore complex (NPC) reformation / regulation of mitotic nuclear division / condensed nuclear chromosome / spindle assembly / nucleosome binding / nucleosomal DNA binding / viral process / mitotic spindle organization / guanyl-nucleotide exchange factor activity / chromosome segregation / G1/S transition of mitotic cell cycle / small GTPase binding / chromosome / histone binding / protein heterodimerization activity / cell division / chromatin binding / chromatin / protein-containing complex / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Dong, C. / Tempel, W. / Li, Y. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Commun Biol / Year: 2018 Title: An asparagine/glycine switch governs product specificity of human N-terminal methyltransferase NTMT2. Authors: Dong, C. / Dong, G. / Li, L. / Zhu, L. / Tempel, W. / Liu, Y. / Huang, R. / Min, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dub.cif.gz | 217.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dub.ent.gz | 172.3 KB | Display | PDB format |
PDBx/mmJSON format | 6dub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dub_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6dub_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6dub_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 6dub_validation.cif.gz | 34.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/6dub ftp://data.pdbj.org/pub/pdb/validation_reports/du/6dub | HTTPS FTP |
-Related structure data
Related structure data | 5ubbC 5e1dS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein / Protein/peptide , 2 types, 4 molecules ABEF
#1: Protein | Mass: 25005.688 Da / Num. of mol.: 2 / Fragment: UNP residues 58-278 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METTL11B, C1orf184, NRMT2 / Plasmid: pET28-MKH8SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-V3R References: UniProt: Q5VVY1, protein N-terminal monomethyltransferase #2: Protein/peptide | Mass: 686.843 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P18754*PLUS |
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-Non-polymers , 4 types, 379 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-UNX / #6: 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: 2.51 Å3/Da / Density % sol: 50.97 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 30% PEG2000, 0.1 M potassium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å | ||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jan 23, 2016 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→31.14 Å / Num. obs: 150535 / % possible obs: 96 % / Redundancy: 6.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.032 / Rrim(I) all: 0.081 / Net I/σ(I): 11 / Num. measured all: 914436 / Scaling rejects: 235 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5E1D Resolution: 1.2→31.1 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.144 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 83.51 Å2 / Biso mean: 16.091 Å2 / Biso min: 5.74 Å2
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Refinement step | Cycle: final / Resolution: 1.2→31.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Total num. of bins used: 20
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