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Yorodumi- PDB-6kdq: Crystal structure of human NRMT1 in complex with alpha-N-monometh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kdq | ||||||
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Title | Crystal structure of human NRMT1 in complex with alpha-N-monomethylated human CENP-A peptide | ||||||
Components |
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Keywords | TRANSFERASE / core methyltransferase fold | ||||||
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 / CENP-A containing chromatin assembly / protein methyltransferase activity / protein localization to chromosome, centromeric region / kinetochore assembly ...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 / CENP-A containing chromatin assembly / protein methyltransferase activity / protein localization to chromosome, centromeric region / kinetochore assembly / condensed chromosome, centromeric region / spindle organization / histone methyltransferase activity / establishment of mitotic spindle orientation / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / mitotic cytokinesis / chromosome, centromeric region / pericentric heterochromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Deposition of new CENPA-containing nucleosomes at the centromere / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / chromosome segregation / RHO GTPases Activate Formins / structural constituent of chromatin / Separation of Sister Chromatids / nucleosome / protein heterodimerization activity / chromatin binding / DNA binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 Å | ||||||
Authors | Yue, Y. / Li, H. | ||||||
Citation | Journal: to be published Title: Substrate engagement regulates state-specific alpha-N methylation of CENP-A by NRMT2 Authors: Wu, R. / Yue, Y. / Zheng, X. / Li, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kdq.cif.gz | 231.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kdq.ent.gz | 182.7 KB | Display | PDB format |
PDBx/mmJSON format | 6kdq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kdq_validation.pdf.gz | 1003.6 KB | Display | wwPDB validaton report |
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Full document | 6kdq_full_validation.pdf.gz | 1004 KB | Display | |
Data in XML | 6kdq_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | 6kdq_validation.cif.gz | 39.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/6kdq ftp://data.pdbj.org/pub/pdb/validation_reports/kd/6kdq | HTTPS FTP |
-Related structure data
Related structure data | 6kdsC 5cvdS 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
#1: Protein | Mass: 27589.418 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NTMT1,NRMT1 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9BV86, protein N-terminal methyltransferase #2: Protein/peptide | Mass: 902.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P49450*PLUS #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.19 Å3/Da / Density % sol: 43.85 % / Mosaicity: 2.315 ° / Mosaicity esd: 0.014 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 5.7 Details: 0.2M Ammonium acetate, 0.1M Sodium citrate dehydrate pH 5.7, 31% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 31, 2015 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.499→50 Å / Num. obs: 77499 / % possible obs: 98.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.044 / Rrim(I) all: 0.089 / Χ2: 1.652 / Net I/σ(I): 13.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CVD Resolution: 1.499→28.229 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.3
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.11 Å2 / Biso mean: 20.2055 Å2 / Biso min: 8.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.499→28.229 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 14.4345 Å / Origin y: -1.9531 Å / Origin z: 14.1057 Å
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Refinement TLS group |
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