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- PDB-6ljk: Crystal structure of human Sirt5 in complex with an internally qu... -

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Basic information

Entry
Database: PDB / ID: 6ljk
TitleCrystal structure of human Sirt5 in complex with an internally quenched fluorescent substrate GluIQF
Components
  • BE2-SER-ALA-ILE-LYS-SER-NIY-GLY-SET
  • NAD-dependent protein deacylase sirtuin-5, mitochondrial
KeywordsTRANSFERASE / Sirt5 / inhibitor / HYDROLASE
Function / homology
Function and homology information


protein demalonylation / protein deglutarylation / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent protein lysine deacetylase activity ...protein demalonylation / protein deglutarylation / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent protein lysine deacetylase activity / protein deacetylation / histone deacetylase activity, NAD-dependent / negative regulation of cardiac muscle cell apoptotic process / negative regulation of reactive oxygen species metabolic process / NAD+ binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to ischemia / mitochondrion organization / response to nutrient levels / Transcriptional activation of mitochondrial biogenesis / mitochondrial intermembrane space / mitochondrial inner membrane / mitochondrial matrix / mitochondrion / zinc ion binding / nucleus / cytosol
Similarity search - Function
Sirtuin, class III / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
GLUTARIC ACID / NAD-dependent protein deacylase sirtuin-5, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.394 Å
AuthorsChen, Q. / Yu, Y.
CitationJournal: Eur.J.Med.Chem. / Year: 2020
Title: Sensitive fluorogenic substrates for sirtuin deacylase inhibitor discovery.
Authors: Yang, L.L. / Wang, H.L. / Yan, Y.H. / Liu, S. / Yu, Z.J. / Huang, M.Y. / Luo, Y. / Zheng, X. / Yu, Y. / Li, G.B.
History
DepositionDec 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent protein deacylase sirtuin-5, mitochondrial
B: BE2-SER-ALA-ILE-LYS-SER-NIY-GLY-SET
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7655
Polymers30,5452
Non-polymers2213
Water6,990388
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-7 kcal/mol
Surface area12470 Å2
Unit cell
Length a, b, c (Å)33.997, 72.754, 55.876
Angle α, β, γ (deg.)90.000, 97.060, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein NAD-dependent protein deacylase sirtuin-5, mitochondrial / Regulatory protein SIR2 homolog 5 / SIR2-like protein 5


Mass: 29568.674 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT5, SIR2L5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NXA8, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein/peptide BE2-SER-ALA-ILE-LYS-SER-NIY-GLY-SET


Mass: 976.022 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 391 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GUA / GLUTARIC ACID


Mass: 132.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25%-27% (v/v) PEG 3350, 0.1 M MES, pH 5.5-6.0, 0.1-0.2 M NaCl
PH range: 5.5-6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.39→44.102 Å / Num. obs: 47791 / % possible obs: 88.84 % / Redundancy: 4.02 % / Biso Wilson estimate: 10.14 Å2 / CC1/2: 0.99 / Net I/σ(I): 17.24
Reflection shellResolution: 1.39→1.48 Å / Num. unique obs: 7194 / CC1/2: 0.97

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XHS

5xhs


Resolution: 1.394→44.102 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 14.57
RfactorNum. reflection% reflection
Rfree0.1582 1431 3 %
Rwork0.1222 --
obs0.1233 47773 88.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 65.47 Å2 / Biso mean: 15.0322 Å2 / Biso min: 3.3 Å2
Refinement stepCycle: final / Resolution: 1.394→44.102 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 146 391 2595
Biso mean--22.09 28.58 -
Num. residues----269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092310
X-RAY DIFFRACTIONf_angle_d1.113147
X-RAY DIFFRACTIONf_chiral_restr0.082337
X-RAY DIFFRACTIONf_plane_restr0.007423
X-RAY DIFFRACTIONf_dihedral_angle_d19.441837
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.394-1.44390.16821250.1521405978
1.4439-1.50170.17281440.1259468390
1.5017-1.570.16191380.0987447786
1.57-1.65280.13561450.0968469990
1.6528-1.75640.14691460.1034474791
1.7564-1.8920.14681400.1076450787
1.892-2.08240.14861490.1063484393
2.0824-2.38370.14691440.1109465289
2.3837-3.00310.15311510.1238488794
3.0031-44.10.18091490.151478890

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