+Open data
-Basic information
Entry | Database: PDB / ID: 6l71 | ||||||
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Title | Sirtuin 2 demyristoylation native intermediate I & II mixture | ||||||
Components |
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Keywords | TRANSFERASE / Sirtuin / myristoylation / intermediate | ||||||
Function / homology | Function and homology information cellular response to caloric restriction / negative regulation of oligodendrocyte progenitor proliferation / cellular lipid catabolic process / negative regulation of striated muscle tissue development / positive regulation of meiotic nuclear division / NAD-dependent histone H4K16 deacetylase activity / positive regulation of attachment of spindle microtubules to kinetochore / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / paranodal junction ...cellular response to caloric restriction / negative regulation of oligodendrocyte progenitor proliferation / cellular lipid catabolic process / negative regulation of striated muscle tissue development / positive regulation of meiotic nuclear division / NAD-dependent histone H4K16 deacetylase activity / positive regulation of attachment of spindle microtubules to kinetochore / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / paranodal junction / tubulin deacetylation / lateral loop / NLRP3 inflammasome complex assembly / peptidyl-lysine deacetylation / mitotic nuclear membrane reassembly / negative regulation of NLRP3 inflammasome complex assembly / tubulin deacetylase activity / regulation of exit from mitosis / paranode region of axon / Schmidt-Lanterman incisure / NAD-dependent protein lysine deacetylase activity / positive regulation of fatty acid biosynthetic process / myelination in peripheral nervous system / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / chromatin silencing complex / NAD-dependent histone deacetylase activity / Initiation of Nuclear Envelope (NE) Reformation / protein deacetylation / regulation of phosphorylation / positive regulation of oocyte maturation / juxtaparanode region of axon / protein lysine deacetylase activity / meiotic spindle / response to redox state / regulation of myelination / histone acetyltransferase binding / histone deacetylase activity / positive regulation of DNA binding / negative regulation of fat cell differentiation / negative regulation of peptidyl-threonine phosphorylation / positive regulation of execution phase of apoptosis / glial cell projection / positive regulation of cell division / NAD+-protein poly-ADP-ribosyltransferase activity / NAD+ binding / subtelomeric heterochromatin formation / negative regulation of reactive oxygen species metabolic process / heterochromatin / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cellular response to epinephrine stimulus / substantia nigra development / centriole / epigenetic regulation of gene expression / negative regulation of autophagy / meiotic cell cycle / ubiquitin binding / heterochromatin formation / negative regulation of protein catabolic process / mitotic spindle / autophagy / histone deacetylase binding / spindle / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / myelin sheath / chromosome / cellular response to oxidative stress / midbody / cellular response to hypoxia / growth cone / perikaryon / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription factor binding / microtubule / chromosome, telomeric region / regulation of cell cycle / cell division / innate immune response / negative regulation of DNA-templated transcription / centrosome / chromatin binding / nucleolus / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.109 Å | ||||||
Authors | Chen, L.F. | ||||||
Funding support | Hong Kong, 1items
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Citation | Journal: To Be Published Title: Sirtuin 2 protein with H3K18 myristoylated peptide Authors: Chen, L.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l71.cif.gz | 89.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l71.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 6l71.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/6l71 ftp://data.pdbj.org/pub/pdb/validation_reports/l7/6l71 | HTTPS FTP |
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-Related structure data
Related structure data | 6l65C 6l66C 6l72C 4r8mS 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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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AC
#1: Protein | Mass: 34404.691 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT2, SIR2L, SIR2L2 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 References: UniProt: Q8IXJ6, protein acetyllysine N-acetyltransferase |
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#2: Protein/peptide | Mass: 713.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 226 molecules
#3: Chemical | ChemComp-NCA / |
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#4: Chemical | ChemComp-YOY / [[( |
#5: Chemical | ChemComp-YDD / [[( |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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Nonpolymer details | YDD and YOY are in alternate confirmations of each other. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.32 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES, pH 6.5, 6%-20% (w/v) PEG 10000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.109→50 Å / Num. obs: 18062 / % possible obs: 96.7 % / Redundancy: 5.9 % / CC1/2: 0.989 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.109→2.15 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 712 / CC1/2: 0.601 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4R8M Resolution: 2.109→27.924 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.47
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.95 Å2 / Biso mean: 34.6187 Å2 / Biso min: 7.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.109→27.924 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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