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- PDB-3zgo: Re-refined structure of the human Sirt2 apoform -

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Basic information

Entry
Database: PDB / ID: 3zgo
TitleRe-refined structure of the human Sirt2 apoform
ComponentsNAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-2
KeywordsHYDROLASE / NAD+-DEPENDENT DEACETYLASE / SIRTUIN
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 ...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 / positive regulation of fatty acid biosynthetic process / NAD-dependent protein lysine deacetylase activity / myelination in peripheral nervous system / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / chromatin silencing complex / NAD-dependent histone deacetylase activity / 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 / regulation of myelination / histone deacetylase activity / negative regulation of fat cell differentiation / histone acetyltransferase binding / 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 / spindle / negative regulation of protein catabolic process / mitotic 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 / 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
Sirtuin, class I / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily ...Sirtuin, class I / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ETHANOL / TRIETHYLENE GLYCOL / NAD-dependent protein deacetylase sirtuin-2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.63 Å
AuthorsMoniot, S. / Steegborn, C.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Structure of the Histone Deacetylase Sirt2.
Authors: Finnin, M.S. / Donigian, J.R. / Pavletich, N.P.
History
DepositionDec 18, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2Oct 18, 2017Group: Data collection / Category: diffrn_radiation / diffrn_source / Item: _diffrn_source.pdbx_wavelength_list
Revision 1.3Oct 25, 2017Group: Data collection / Category: diffrn_radiation / diffrn_radiation_wavelength / Item: _diffrn_radiation.wavelength_id
Revision 1.4Nov 6, 2019Group: Data collection / Database references / Other / Category: pdbx_database_related / pdbx_database_status / Item: _pdbx_database_status.status_code_sf
Remark 0THIS ENTRY 3ZGO REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R1J8FSF) ...THIS ENTRY 3ZGO REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R1J8FSF) DETERMINED BY AUTHORS OF THE PDB ENTRY 1J8F: N.P.PAVLETICH,M.S.FINNIN,J.R.DONIGIAN

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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
B: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-2
C: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,61816
Polymers109,9803
Non-polymers1,63813
Water19,4921082
1
A: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2205
Polymers36,6601
Non-polymers5604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9224
Polymers36,6601
Non-polymers2623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4767
Polymers36,6601
Non-polymers8166
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.940, 119.070, 218.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-2 / SIRTUIN 2 / ISOFORM 1 / REGULATORY PROTEIN SIR2 HOMOLOG 2 / SIR2-LIKE PROTEIN 2


Mass: 36660.125 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-4T3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8IXJ6, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 6 types, 1095 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1082 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.24 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1J8F.

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
ROTATING ANODE11.54
SYNCHROTRONCHESS F120.98
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
20.981
ReflectionObserved criterion σ(I): 0

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Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 1.63→19.84 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.113 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.19503 2441 2 %RANDOM
Rwork0.16785 ---
obs0.16839 120106 95.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.055 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2--0.13 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.63→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7451 0 87 1082 8620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0198336
X-RAY DIFFRACTIONr_bond_other_d0.0010.027876
X-RAY DIFFRACTIONr_angle_refined_deg1.7931.98711298
X-RAY DIFFRACTIONr_angle_other_deg0.8193.00218287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.81551063
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23523.801371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.849151485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0361554
X-RAY DIFFRACTIONr_chiral_restr0.120.21179
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0219558
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021900
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_it1.5250.8854091
X-RAY DIFFRACTIONr_mcbond_other1.5220.8844090
X-RAY DIFFRACTIONr_mcangle_it2.3231.3165204
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5313.5274245
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded26.57853
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 106 -
Rwork0.258 5113 -
obs--56.13 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4068-0.2790.20281.6047-0.39120.53480.0045-0.019-0.01450.13210.034-0.04410.0013-0.0525-0.03850.09180.0137-0.01480.0527-0.00880.039422.65726.6632.639
20.25010.2180.08272.6787-1.05451.1450.01560.0168-0.02190.0594-0.0341-0.4619-0.03620.05030.01850.0860.0055-0.0640.06660.02610.227238.832.27430.235
30.6975-0.6208-0.33930.73520.10430.52740.0020.01940.12150.00070.0024-0.0998-0.06090.0165-0.00440.10160.0061-0.02980.0684-0.01420.080383.59357.5238.199
40.3023-0.3147-0.43820.71270.55791.1192-0.07240.0157-0.11590.0943-0.04530.1270.0774-0.13670.11770.1079-0.01110.00960.1012-0.01690.084172.38744.40141.533
50.29090.16420.00041.16350.02720.171-0.0093-0.0219-0.02490.01690.01930.0361-0.0121-0.004-0.01010.08110.0025-0.01640.0169-0.01120.061969.15423.3540.808
60.8866-0.06230.67810.2889-0.04961.2774-0.00580.0628-0.0049-0.00050.03640.0285-0.0898-0.0424-0.03060.0945-0.0098-0.00960.0358-0.00190.062273.12339.261-3.519
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 261
2X-RAY DIFFRACTION2A262 - 356
3X-RAY DIFFRACTION3B32 - 265
4X-RAY DIFFRACTION4B266 - 356
5X-RAY DIFFRACTION5C54 - 241
6X-RAY DIFFRACTION6C242 - 356

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