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- PDB-6l65: Sirtuin 2 protein with H3K18 myristoylated peptide -

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Basic information

Entry
Database: PDB / ID: 6l65
TitleSirtuin 2 protein with H3K18 myristoylated peptide
Components
  • NAD-dependent protein deacetylase sirtuin-2
  • PRO-ARG-LYS-GLN-LEU
KeywordsTRANSFERASE / Sirtuin / myristoylation
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 / tubulin deacetylation / NAD-dependent protein demyristoylase activity ...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 / tubulin deacetylation / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / paranodal junction / lateral loop / NLRP3 inflammasome complex assembly / peptidyl-lysine deacetylation / mitotic nuclear membrane reassembly / negative regulation of NLRP3 inflammasome complex assembly / tubulin deacetylase activity / paranode region of axon / Schmidt-Lanterman incisure / regulation of exit from mitosis / myelination in peripheral nervous system / positive regulation of fatty acid biosynthetic process / NAD-dependent protein lysine deacetylase activity / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / chromatin silencing complex / regulation of phosphorylation / Initiation of Nuclear Envelope (NE) Reformation / protein deacetylation / juxtaparanode region of axon / positive regulation of oocyte maturation / protein lysine deacetylase activity / meiotic spindle / response to redox state / histone deacetylase activity / regulation of myelination / histone acetyltransferase binding / negative regulation of fat cell differentiation / positive regulation of execution phase of apoptosis / negative regulation of peptidyl-threonine phosphorylation / glial cell projection / subtelomeric heterochromatin formation / positive regulation of cell division / NAD+ ADP-ribosyltransferase activity / NAD+ binding / negative regulation of reactive oxygen species metabolic process / positive regulation of DNA binding / heterochromatin / heterochromatin formation / epigenetic regulation of gene expression / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cellular response to epinephrine stimulus / substantia nigra development / centriole / negative regulation of autophagy / meiotic cell cycle / ubiquitin binding / negative regulation of protein catabolic process / mitotic spindle / spindle / autophagy / histone deacetylase binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / myelin sheath / cellular response to oxidative stress / chromosome / midbody / growth cone / cellular response to hypoxia / 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 / centrosome / negative regulation of DNA-templated transcription / 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
Sirtuin, class I / Sirtuin, catalytic core small domain superfamily / Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
MYRISTIC ACID / NAD-dependent protein deacetylase sirtuin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChen, L.F.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)HKU/C7037-14G Hong Kong
CitationJournal: To Be Published
Title: Sirtuin 2 protein with H3K18 myristoylated peptide
Authors: Chen, L.F.
History
DepositionOct 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent protein deacetylase sirtuin-2
C: PRO-ARG-LYS-GLN-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6284
Polymers35,3342
Non-polymers2942
Water6,792377
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint3 kcal/mol
Surface area14300 Å2
Unit cell
Length a, b, c (Å)36.062, 73.399, 55.693
Angle α, β, γ (deg.)90.000, 93.860, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NAD-dependent protein deacetylase sirtuin-2 / Regulatory protein SIR2 homolog 2 / SIR2-like protein 2


Mass: 34691.016 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 (E. coli)
References: UniProt: Q8IXJ6, protein acetyllysine N-acetyltransferase
#2: Protein/peptide PRO-ARG-LYS-GLN-LEU


Mass: 642.790 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 293.1 K / Method: evaporation / pH: 6.5 / Details: 0.1M MES, pH 6.5, 6%-20% (w/v) PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97906 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97906 Å / Relative weight: 1
ReflectionResolution: 1.58→55.6 Å / Num. obs: 29350 / % possible obs: 74 % / Redundancy: 6.06 % / CC1/2: 0.992 / Net I/σ(I): 11.7
Reflection shellResolution: 1.58→1.66 Å / Num. unique obs: 1169 / CC1/2: 0.522

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R8M

4r8m


Resolution: 1.8→55.594 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.14
RfactorNum. reflection% reflection
Rfree0.2184 1203 4.8 %
Rwork0.1769 --
obs0.1789 25060 93.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.54 Å2 / Biso mean: 20.5053 Å2 / Biso min: 1.17 Å2
Refinement stepCycle: final / Resolution: 1.8→55.594 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2334 0 15 377 2726
Biso mean--24.86 30.51 -
Num. residues----292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072450
X-RAY DIFFRACTIONf_angle_d0.9553307
X-RAY DIFFRACTIONf_chiral_restr0.053360
X-RAY DIFFRACTIONf_plane_restr0.006421
X-RAY DIFFRACTIONf_dihedral_angle_d9.7582069
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.87210.36161040.35185167
1.8721-1.95730.33411230.2401228981
1.9573-2.06050.21221340.1963276598
2.0605-2.18960.26251450.17952813100
2.1896-2.35860.21151430.1743282399
2.3586-2.5960.20781330.1692282999
2.596-2.97160.23411440.1667282799
2.9716-3.74380.19691390.1553279698
3.7438-55.570.16181380.1529286498
Refinement TLS params.Method: refined / Origin x: -8.3544 Å / Origin y: 6.3871 Å / Origin z: -8.6197 Å
111213212223313233
T0.0155 Å20.0065 Å2-0.0101 Å2-0.0182 Å2-0.0015 Å2--0.0021 Å2
L0.2767 °2-0.0667 °2-0.1669 °2-0.2305 °20.1164 °2--0.2908 °2
S-0.0073 Å °0.0722 Å °-0.1097 Å °-0.03 Å °0.0048 Å °-0.0287 Å °-0.0309 Å °-0.1203 Å °0.0213 Å °
Refinement TLS groupSelection details: all

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