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- PDB-5x16: Sirt6 apo structure -

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Basic information

Entry
Database: PDB / ID: 5x16
TitleSirt6 apo structure
ComponentsNAD-dependent protein deacetylase sirtuin-6
KeywordsHYDROLASE / apo
Function / homology
Function and homology information


histone H3K56 deacetylase activity, NAD-dependent / ketone biosynthetic process / histone H3K18 deacetylase activity, NAD-dependent / histone H3K9 deacetylase activity, hydrolytic mechanism / histone H3K9 deacetylase activity, NAD-dependent / protein delipidation / NAD+-protein-lysine ADP-ribosyltransferase activity / chromosome, subtelomeric region / regulation of lipid catabolic process / positive regulation of protein localization to chromatin ...histone H3K56 deacetylase activity, NAD-dependent / ketone biosynthetic process / histone H3K18 deacetylase activity, NAD-dependent / histone H3K9 deacetylase activity, hydrolytic mechanism / histone H3K9 deacetylase activity, NAD-dependent / protein delipidation / NAD+-protein-lysine ADP-ribosyltransferase activity / chromosome, subtelomeric region / regulation of lipid catabolic process / positive regulation of protein localization to chromatin / NAD+-protein-arginine ADP-ribosyltransferase activity / DNA damage sensor activity / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / positive regulation of stem cell differentiation / negative regulation of D-glucose import across plasma membrane / positive regulation of chondrocyte proliferation / transposable element silencing / NAD-dependent protein lysine deacetylase activity / cardiac muscle cell differentiation / protein acetyllysine N-acetyltransferase / pericentric heterochromatin formation / histone deacetylase activity, NAD-dependent / protein deacetylation / positive regulation of blood vessel branching / protein localization to site of double-strand break / negative regulation of glycolytic process / positive regulation of vascular endothelial cell proliferation / TORC2 complex binding / negative regulation of protein import into nucleus / regulation of double-strand break repair via homologous recombination / regulation of protein secretion / DNA repair-dependent chromatin remodeling / positive regulation of double-strand break repair / positive regulation of stem cell proliferation / negative regulation of gene expression, epigenetic / lncRNA binding / NAD+-protein mono-ADP-ribosyltransferase activity / positive regulation of stem cell population maintenance / positive regulation of telomere maintenance / negative regulation of cellular senescence / Transferases; Glycosyltransferases; Pentosyltransferases / regulation of lipid metabolic process / negative regulation of transcription elongation by RNA polymerase II / NAD+ poly-ADP-ribosyltransferase activity / NAD+ binding / negative regulation of gluconeogenesis / positive regulation of fat cell differentiation / subtelomeric heterochromatin formation / site of DNA damage / pericentric heterochromatin / regulation of protein localization to plasma membrane / nucleosome binding / response to UV / negative regulation of protein localization to chromatin / nucleotidyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of protein export from nucleus / determination of adult lifespan / circadian regulation of gene expression / positive regulation of insulin secretion / regulation of circadian rhythm / chromatin DNA binding / base-excision repair / Pre-NOTCH Transcription and Translation / protein destabilization / positive regulation of fibroblast proliferation / protein import into nucleus / transcription corepressor activity / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / glucose homeostasis / positive regulation of cold-induced thermogenesis / site of double-strand break / Processing of DNA double-strand break ends / damaged DNA binding / chromatin remodeling / negative regulation of cell population proliferation / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / protein homodimerization activity / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Rubrerythrin, domain 2 - #200 / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / Rubrerythrin, domain 2 / DHS-like NAD/FAD-binding domain superfamily / Single Sheet ...Rubrerythrin, domain 2 - #200 / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / Rubrerythrin, domain 2 / DHS-like NAD/FAD-binding domain superfamily / Single Sheet / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-AR6 / TERTIARY-BUTYL ALCOHOL / NAD-dependent protein deacylase sirtuin-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsZhang, J. / Huang, Z. / Song, K.
CitationJournal: To Be Published
Title: Sirt6 apo structure
Authors: Zhang, J. / Huang, Z. / Song, K.
History
DepositionJan 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8686
Polymers35,0031
Non-polymers8655
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-1 kcal/mol
Surface area14360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.565, 68.138, 117.314
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NAD-dependent protein deacetylase sirtuin-6 / Regulatory protein SIR2 homolog 6 / SIR2-like protein 6


Mass: 35003.105 Da / Num. of mol.: 1 / Fragment: UNP residues 3-318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT6, SIR2L6 / Production host: Homo sapiens (human)
References: UniProt: Q8N6T7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 5 types, 229 molecules

#2: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL


Mass: 74.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium citrate tribasic dihydrate pH 5.6, 35% v/v tert-Butanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: CMOS / Date: May 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 88468 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 18.927
Reflection shellResolution: 1.97→2.01 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 2.186 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data collection
SCALEPACKdata processing
REFMACmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.87 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.163 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2316 1149 4.9 %RANDOM
Rwork0.18408 ---
obs0.18654 22077 93.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.496 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-0 Å2-0 Å2
2---0.45 Å20 Å2
3---0.85 Å2
Refinement stepCycle: 1 / Resolution: 1.97→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2282 0 53 224 2559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192421
X-RAY DIFFRACTIONr_bond_other_d0.0020.022350
X-RAY DIFFRACTIONr_angle_refined_deg1.5462.0043291
X-RAY DIFFRACTIONr_angle_other_deg0.9943.0015406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8715298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91122.136103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36815408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7341528
X-RAY DIFFRACTIONr_chiral_restr0.0830.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212665
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02536
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8113.1161188
X-RAY DIFFRACTIONr_mcbond_other1.8093.111185
X-RAY DIFFRACTIONr_mcangle_it2.8774.6551486
X-RAY DIFFRACTIONr_mcangle_other2.8774.661487
X-RAY DIFFRACTIONr_scbond_it2.293.4561233
X-RAY DIFFRACTIONr_scbond_other2.2893.4561233
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7555.061806
X-RAY DIFFRACTIONr_long_range_B_refined6.4625.4082787
X-RAY DIFFRACTIONr_long_range_B_other6.37225.0862694
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.972→2.024 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 69 -
Rwork0.27 1396 -
obs--80.67 %

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