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Yorodumi- PDB-5e2a: Crystal structure of NTMT1 in complex with N-terminally methylate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e2a | ||||||
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Title | Crystal structure of NTMT1 in complex with N-terminally methylated SPKRIA peptide | ||||||
Components |
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Keywords | TRANSFERASE / methyl transferase / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information N-terminal peptidyl-glycine methylation / N-terminal peptidyl-serine dimethylation / N-terminal peptidyl-serine trimethylation / protein N-terminal methyltransferase / N-terminal peptidyl-proline dimethylation / N-terminal protein N-methyltransferase activity / mitotic nuclear membrane reassembly / protein methyltransferase activity / sulfate binding / Rev-mediated nuclear export of HIV RNA ...N-terminal peptidyl-glycine methylation / N-terminal peptidyl-serine dimethylation / N-terminal peptidyl-serine trimethylation / protein N-terminal methyltransferase / N-terminal peptidyl-proline dimethylation / N-terminal protein N-methyltransferase activity / mitotic nuclear membrane reassembly / protein methyltransferase activity / 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 / spindle organization / histone methyltransferase activity / nucleosomal DNA binding / nucleosome binding / spindle assembly / viral process / guanyl-nucleotide exchange factor activity / mitotic spindle organization / condensed nuclear chromosome / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.75 Å | ||||||
Authors | Dong, C. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Genes Dev. / Year: 2015 Title: Structural basis for substrate recognition by the human N-terminal methyltransferase 1. Authors: Dong, C. / Mao, Y. / Tempel, W. / Qin, S. / Li, L. / Loppnau, P. / 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 | 5e2a.cif.gz | 209.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e2a.ent.gz | 165.4 KB | Display | PDB format |
PDBx/mmJSON format | 5e2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/5e2a ftp://data.pdbj.org/pub/pdb/validation_reports/e2/5e2a | HTTPS FTP |
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-Related structure data
Related structure data | 5e1bC 5e1dC 5e1mC 5e1oC 5e2bC 2ex4S C: citing same article (ref.) 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
-Protein / Protein/peptide , 2 types, 4 molecules ABDE
#1: Protein | Mass: 27320.074 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NTMT1, C9orf32, METTL11A, NRMT, NRMT1, AD-003 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V3R References: UniProt: Q9BV86, protein N-terminal methyltransferase #2: Protein/peptide | Mass: 686.843 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P18754*PLUS |
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-Non-polymers , 4 types, 465 molecules
#3: Chemical | #4: Chemical | ChemComp-GOL / #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: 2.98 Å3/Da / Density % sol: 58.79 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 26% PEG3350, 16% tacsimate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Aug 8, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→29.62 Å / Num. obs: 70896 / % possible obs: 100 % / Redundancy: 20.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.028 / Rrim(I) all: 0.129 / Net I/σ(I): 27.6 / Num. measured all: 1473712 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdbid 2ex4 Resolution: 1.75→29.6 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.161 / WRfactor Rwork: 0.138 / FOM work R set: 0.8996 / SU B: 2.969 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0808 / SU Rfree: 0.0819 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Coot was used for interactive model building. Molprobity was used for geometry validation.
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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: 48.69 Å2 / Biso mean: 17.264 Å2 / Biso min: 7.13 Å2
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Refinement step | Cycle: final / Resolution: 1.75→29.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 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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