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- PDB-3k35: Crystal Structure of Human SIRT6 -

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Basic information

Entry
Database: PDB / ID: 3k35
TitleCrystal Structure of Human SIRT6
ComponentsNAD-dependent deacetylase sirtuin-6
KeywordsHYDROLASE / Rossmann fold / Zn-binding domain / Structural Genomics / Structural Genomics Consortium / SGC / ADP-ribosylation / Metal-binding / NAD / NADP / Nucleus / Phosphoprotein
Function / homology
Function and homology information


NAD-dependent histone H3K56 deacetylase activity / NAD-dependent histone H3K18 deacetylase activity / NAD-dependent histone H3K9 deacetylase activity / protein delipidation / ketone biosynthetic process / regulation of lipid catabolic process / NAD+-protein-lysine ADP-ribosyltransferase activity / chromosome, subtelomeric region / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity ...NAD-dependent histone H3K56 deacetylase activity / NAD-dependent histone H3K18 deacetylase activity / NAD-dependent histone H3K9 deacetylase activity / protein delipidation / ketone biosynthetic process / regulation of lipid catabolic process / NAD+-protein-lysine ADP-ribosyltransferase activity / chromosome, subtelomeric region / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / NAD+-protein-arginine ADP-ribosyltransferase activity / positive regulation of protein localization to chromatin / DNA damage sensor activity / positive regulation of stem cell differentiation / positive regulation of blood vessel branching / NAD-dependent protein lysine deacetylase activity / retrotransposon silencing / protein acetyllysine N-acetyltransferase / cardiac muscle cell differentiation / positive regulation of chondrocyte proliferation / pericentric heterochromatin formation / positive regulation of telomere maintenance / protein deacetylation / negative regulation of glucose import / protein localization to site of double-strand break / NAD-dependent histone deacetylase activity / TORC2 complex binding / lncRNA binding / negative regulation of glycolytic process / negative regulation of protein localization to chromatin / positive regulation of double-strand break repair / DNA repair-dependent chromatin remodeling / positive regulation of vascular endothelial cell proliferation / negative regulation of protein import into nucleus / negative regulation of gene expression, epigenetic / regulation of double-strand break repair via homologous recombination / positive regulation of stem cell population maintenance / positive regulation of stem cell proliferation / regulation of protein secretion / negative regulation of transcription elongation by RNA polymerase II / NAD+-protein ADP-ribosyltransferase activity / negative regulation of cellular senescence / site of DNA damage / regulation of lipid metabolic process / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity / NAD+ binding / subtelomeric heterochromatin formation / positive regulation of fat cell differentiation / regulation of protein localization to plasma membrane / pericentric heterochromatin / negative regulation of gluconeogenesis / response to UV / nucleosome binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / nucleotidyltransferase activity / positive regulation of protein export from nucleus / determination of adult lifespan / circadian regulation of gene expression / protein destabilization / base-excision repair / regulation of circadian rhythm / positive regulation of insulin secretion / chromatin DNA binding / Pre-NOTCH Transcription and Translation / transcription corepressor activity / positive regulation of fibroblast proliferation / 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 / intracellular membrane-bounded organelle / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / protein homodimerization activity / 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 / Rossmann fold ...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
ADENOSINE-5-DIPHOSPHORIBOSE / NAD-dependent protein deacylase sirtuin-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPan, P.W. / Dong, A. / Qiu, W. / Loppnau, P. / Wang, J. / Ravichandran, M. / Bochkarev, A. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. ...Pan, P.W. / Dong, A. / Qiu, W. / Loppnau, P. / Wang, J. / Ravichandran, M. / Bochkarev, A. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Min, J. / Edwards, A.M. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure and biochemical functions of SIRT6.
Authors: Pan, P.W. / Feldman, J.L. / Devries, M.K. / Dong, A. / Edwards, A.M. / Denu, J.M.
History
DepositionOct 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 1, 2017Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent deacetylase sirtuin-6
B: NAD-dependent deacetylase sirtuin-6
C: NAD-dependent deacetylase sirtuin-6
D: NAD-dependent deacetylase sirtuin-6
E: NAD-dependent deacetylase sirtuin-6
F: NAD-dependent deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,88149
Polymers210,8836
Non-polymers4,99743
Water17,312961
1
A: NAD-dependent deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,15610
Polymers35,1471
Non-polymers1,0099
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NAD-dependent deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9648
Polymers35,1471
Non-polymers8177
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NAD-dependent deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8687
Polymers35,1471
Non-polymers7216
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NAD-dependent deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9648
Polymers35,1471
Non-polymers8177
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: NAD-dependent deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9648
Polymers35,1471
Non-polymers8177
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: NAD-dependent deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9648
Polymers35,1471
Non-polymers8177
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
F: NAD-dependent deacetylase sirtuin-6
hetero molecules

A: NAD-dependent deacetylase sirtuin-6
hetero molecules

C: NAD-dependent deacetylase sirtuin-6
hetero molecules

E: NAD-dependent deacetylase sirtuin-6
hetero molecules

B: NAD-dependent deacetylase sirtuin-6
D: NAD-dependent deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,88149
Polymers210,8836
Non-polymers4,99743
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
crystal symmetry operation2_554-x,y+1/2,-z-11
crystal symmetry operation2_555-x,y+1/2,-z1
identity operation1_555x,y,z1
Buried area23430 Å2
ΔGint-298 kcal/mol
Surface area63760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.388, 136.266, 89.260
Angle α, β, γ (deg.)90.00, 119.87, 90.00
Int Tables number4
Space group name H-MP1211
Detailsmonomer

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 35147.238 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIR2L6, SIRT6 / Plasmid: pET28-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon(+) pRARE
References: UniProt: Q8N6T7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 5 types, 1004 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 18 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 961 / 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: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 2M NH4SO4, 2%PEG400, 0.1M Bis-Tris pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jul 30, 2009
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. all: 120514 / Num. obs: 120514 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 9.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YC5

1yc5


Resolution: 2→19.95 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.661 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / ESU R: 0.19 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26723 1205 1 %RANDOM
Rwork0.20156 ---
obs0.2022 119269 100 %-
all-119269 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.01 Å2
2---0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12707 0 305 961 13973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02113321
X-RAY DIFFRACTIONr_angle_refined_deg1.5062.00118157
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.49251654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81722.772534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.453152174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.78115122
X-RAY DIFFRACTIONr_chiral_restr0.0940.22067
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219895
X-RAY DIFFRACTIONr_mcbond_it0.7351.58281
X-RAY DIFFRACTIONr_mcangle_it1.313213360
X-RAY DIFFRACTIONr_scbond_it2.16335040
X-RAY DIFFRACTIONr_scangle_it3.4784.54796
LS refinement shellResolution: 2.002→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 83 -
Rwork0.292 8290 -
obs--100 %

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