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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 / histone methacryllysine demethacrylase activity / histone benzoyllysine debenzoylase activity / positive regulation of oocyte maturation / negative regulation of striated muscle tissue development / negative regulation of oligodendrocyte progenitor proliferation / negative regulation of satellite cell differentiation / histone H4K16 deacetylase activity, NAD-dependent / positive regulation of attachment of spindle microtubules to kinetochore / NAD-dependent protein demyristoylase activity ...cellular response to caloric restriction / histone methacryllysine demethacrylase activity / histone benzoyllysine debenzoylase activity / positive regulation of oocyte maturation / negative regulation of striated muscle tissue development / negative regulation of oligodendrocyte progenitor proliferation / negative regulation of satellite cell differentiation / histone H4K16 deacetylase activity, NAD-dependent / positive regulation of attachment of spindle microtubules to kinetochore / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / peptidyl-lysine deacetylation / paranodal junction / positive regulation of meiotic nuclear division / lateral loop / mitotic nuclear membrane reassembly / regulation of exit from mitosis / tubulin deacetylase activity / paranode region of axon / myelination in peripheral nervous system / regulation of phosphorylation / tubulin deacetylation / negative regulation of peptidyl-threonine phosphorylation / Schmidt-Lanterman incisure / regulation of myelination / positive regulation of fatty acid biosynthetic process / protein acetyllysine N-acetyltransferase / NAD-dependent protein lysine deacetylase activity / histone deacetylase activity, NAD-dependent / rDNA heterochromatin formation / juxtaparanode region of axon / Initiation of Nuclear Envelope (NE) Reformation / protein deacetylation / chromatin silencing complex / meiotic spindle / histone deacetylase activity / negative regulation of reactive oxygen species metabolic process / protein lysine deacetylase activity / negative regulation of fat cell differentiation / positive regulation of DNA binding / response to redox state / positive regulation of cell division / histone acetyltransferase binding / NAD+ poly-ADP-ribosyltransferase activity / NAD+ binding / subtelomeric heterochromatin formation / positive regulation of execution phase of apoptosis / lipid catabolic process / glial cell projection / heterochromatin / centriole / cellular response to epinephrine stimulus / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / substantia nigra development / negative regulation of autophagy / ubiquitin binding / negative regulation of protein catabolic process / myelin sheath / meiotic cell cycle / autophagy / epigenetic regulation of gene expression / mitotic spindle / spindle / histone deacetylase binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / growth cone / cellular response to oxidative stress / midbody / heterochromatin formation / cellular response to hypoxia / DNA-binding transcription factor binding / microtubule / proteasome-mediated ubiquitin-dependent protein catabolic process / chromosome / perikaryon / regulation of cell cycle / chromosome, telomeric region / 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 / DNA-templated transcription / nucleoplasm / zinc ion binding / nucleus / 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 ...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
Revision 1.5Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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


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


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


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


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


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

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Details

Has protein modificationY

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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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