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- PDB-5d7n: Crystal structure of human Sirt3 at an improved resolution -

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Basic information

Entry
Database: PDB / ID: 5d7n
TitleCrystal structure of human Sirt3 at an improved resolution
ComponentsNAD-dependent protein deacetylase sirtuin-3, mitochondrial
KeywordsHYDROLASE / Sirtuin 3 / Deacylase
Function / homology
Function and homology information


positive regulation of superoxide dismutase activity / positive regulation of catalase activity / NAD-dependent protein lysine delactylase activity / positive regulation of ceramide biosynthetic process / Maturation of TCA enzymes and regulation of TCA cycle / peptidyl-lysine deacetylation / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / protein deacetylation / histone deacetylase activity, NAD-dependent ...positive regulation of superoxide dismutase activity / positive regulation of catalase activity / NAD-dependent protein lysine delactylase activity / positive regulation of ceramide biosynthetic process / Maturation of TCA enzymes and regulation of TCA cycle / peptidyl-lysine deacetylation / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / protein deacetylation / histone deacetylase activity, NAD-dependent / positive regulation of oxidative phosphorylation / Regulation of FOXO transcriptional activity by acetylation / protein lysine deacetylase activity / cellular response to stress / negative regulation of reactive oxygen species metabolic process / NAD+ binding / Mitochondrial unfolded protein response (UPRmt) / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / aerobic respiration / Transcriptional activation of mitochondrial biogenesis / positive regulation of insulin secretion / negative regulation of ERK1 and ERK2 cascade / sequence-specific DNA binding / mitochondrial matrix / enzyme binding / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
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 ...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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsRumpf, T. / Gerhardt, S. / Einsle, O. / Jung, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationJu295/8-1 Germany
German Research FoundationSFB992 Medical Epigenetics, Project Z02 Germany
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Seeding for sirtuins: microseed matrix seeding to obtain crystals of human Sirt3 and Sirt2 suitable for soaking.
Authors: Rumpf, T. / Gerhardt, S. / Einsle, O. / Jung, M.
History
DepositionAug 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry

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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-3, mitochondrial
B: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
C: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
D: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
E: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
F: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,33723
Polymers187,6086
Non-polymers1,72817
Water22,6451257
1
A: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6766
Polymers31,2681
Non-polymers4085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4403
Polymers31,2681
Non-polymers1722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4403
Polymers31,2681
Non-polymers1722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7705
Polymers31,2681
Non-polymers5024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4843
Polymers31,2681
Non-polymers2162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5283
Polymers31,2681
Non-polymers2602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.990, 143.850, 89.460
Angle α, β, γ (deg.)90.00, 116.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
NAD-dependent protein deacetylase sirtuin-3, mitochondrial / hSIRT3 / Regulatory protein SIR2 homolog 3 / SIR2-like protein 3


Mass: 31268.049 Da / Num. of mol.: 6 / Fragment: UNP residues 118-395
Source method: isolated from a genetically manipulated source
Details: Gly1 originates from TEV cleavage site His2/Met3 originate from NdeI restriction site of the vector
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT3, SIR2L3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NTG7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 8 types, 1274 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1257 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M magnesium chloride, 25 % (w/v) PEG 3350 / PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→33.66 Å / Num. obs: 168813 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 10
Reflection shellResolution: 1.83→1.86 Å / Rmerge(I) obs: 0.815

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
MOLREPphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GLS

3gls


Resolution: 1.83→33.66 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.862 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20316 8479 5 %RANDOM
Rwork0.17494 ---
obs0.17635 160291 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.762 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.12 Å2
2---0.09 Å20 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.83→33.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12775 0 94 1257 14126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01913439
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213096
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.99118337
X-RAY DIFFRACTIONr_angle_other_deg0.8163.00230150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3851703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94922.879587
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.105152172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.01315116
X-RAY DIFFRACTIONr_chiral_restr0.0770.22083
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02115033
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023043
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_it1.0631.5926588
X-RAY DIFFRACTIONr_mcbond_other1.0631.5926587
X-RAY DIFFRACTIONr_mcangle_it1.7912.3788245
X-RAY DIFFRACTIONr_mcangle_other1.7912.3798246
X-RAY DIFFRACTIONr_scbond_it1.4541.8426851
X-RAY DIFFRACTIONr_scbond_other1.4541.8426851
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4272.66210052
X-RAY DIFFRACTIONr_long_range_B_refined5.36914.09815919
X-RAY DIFFRACTIONr_long_range_B_other5.20113.50115361
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.878 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 627 -
Rwork0.272 11866 -
obs--99.89 %
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)
10.1627-0.13650.27320.5479-0.20350.4644-0.02460.0291-0.00350.04590.0387-0.006-0.03840.033-0.01410.0734-0.004-0.01240.10940.03660.018316.1594-0.53093.3116
20.25540.13380.18460.34740.05610.2399-0.0228-0.0040.0486-0.01720.0115-0.01540.04020.04330.01130.0438-0.0028-0.01580.10410.00210.07527.640939.5913-15.1259
30.1588-0.1309-0.1530.14730.02750.46750.0315-0.0131-0.0066-0.0156-0.02510.0156-0.04640.0316-0.00640.0665-0.0390.01180.0969-0.01070.05216.187568.0387-35.8475
40.96280.0204-0.20720.1857-0.02710.0491-0.02440.0758-0.02140.01870.0211-0.0152-0.0056-0.01930.00330.0627-0.0196-0.02620.0904-0.00420.054459.245449.6916-43.1295
50.8146-0.0412-0.03940.319-0.03530.0099-0.01880.1382-0.02410.03580.01770.00530.0010.01170.00120.0374-0.0037-0.0030.1746-0.0130.001910.9803-35.2375-9.7161
60.3398-0.1747-0.1590.11230.00620.85790.0206-0.0113-0.0416-0.02960.03380.03460.0595-0.0049-0.05440.0946-0.0018-0.03760.0485-0.00870.064375.295218.4263-32.5147
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A121 - 400
2X-RAY DIFFRACTION2B122 - 400
3X-RAY DIFFRACTION3C121 - 400
4X-RAY DIFFRACTION4D121 - 400
5X-RAY DIFFRACTION5E122 - 400
6X-RAY DIFFRACTION6F122 - 400

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