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- PDB-5ojn: Sirtuin 4 from Xenopus tropicalis in complex with thioacetyl-ADP-... -

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Basic information

Entry
Database: PDB / ID: 5ojn
TitleSirtuin 4 from Xenopus tropicalis in complex with thioacetyl-ADP-ribose
ComponentsNAD-dependent protein deacylase
KeywordsSIGNALING PROTEIN / Sirtuin / Sirt4 / Deacylase / Mitochondria
Function / homology
Function and homology information


Regulation of pyruvate dehydrogenase (PDH) complex / Transcriptional activation of mitochondrial biogenesis / histone H3K14 deacetylase activity, NAD-dependent / histone H3K9 deacetylase activity, NAD-dependent / histone H4K16 deacetylase activity, NAD-dependent / histone H3K18 deacetylase activity, NAD-dependent / histone H3K56 deacetylase activity, NAD-dependent / histone H3K4 deacetylase activity, NAD-dependent / NAD+ binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups ...Regulation of pyruvate dehydrogenase (PDH) complex / Transcriptional activation of mitochondrial biogenesis / histone H3K14 deacetylase activity, NAD-dependent / histone H3K9 deacetylase activity, NAD-dependent / histone H4K16 deacetylase activity, NAD-dependent / histone H3K18 deacetylase activity, NAD-dependent / histone H3K56 deacetylase activity, NAD-dependent / histone H3K4 deacetylase activity, NAD-dependent / NAD+ binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / mitochondrial matrix / zinc ion binding
Similarity search - Function
Sirtuin, class II / 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
thioacetyl-ADP-ribose / NAD-dependent protein deacylase
Similarity search - Component
Biological speciesXenopus tropicalis (tropical clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPannek, M. / Steegborn, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
Oberfrankenstiftung Germany
CitationJournal: Nat Commun / Year: 2017
Title: Crystal structures of the mitochondrial deacylase Sirtuin 4 reveal isoform-specific acyl recognition and regulation features.
Authors: Pannek, M. / Simic, Z. / Fuszard, M. / Meleshin, M. / Rotili, D. / Mai, A. / Schutkowski, M. / Steegborn, C.
History
DepositionJul 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD-dependent protein deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7833
Polymers32,1001
Non-polymers6832
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Eluates as single, monomeric peak from gelfiltration column
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.970, 74.880, 109.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

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Components

#1: Protein NAD-dependent protein deacylase / Sirtuin 4 / Regulatory protein SIR2 homolog


Mass: 32100.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus tropicalis (tropical clawed frog)
Gene: sirt4, TGas015j14.1-001 / Production host: Escherichia coli (E. coli)
References: UniProt: Q28CB4, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-9X8 / thioacetyl-ADP-ribose


Mass: 617.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H25N5O14P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44.4 % / Description: Diamonds
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.5 M Na/K-tartrate 0.5% PEG5000MME 0.1 M Tris / PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 8, 2015 / Details: Sagitally bended Si111-crystal
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 26585 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.3
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1932 / CC1/2: 0.704 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OJ7

5oj7


Resolution: 1.8→19.74 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.45 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.118 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20883 1330 5 %RANDOM
Rwork0.15528 ---
obs0.15787 25255 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.417 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å2-0 Å2-0 Å2
2--1.27 Å20 Å2
3----0.66 Å2
Refinement stepCycle: 1 / Resolution: 1.8→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 40 179 2372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0192282
X-RAY DIFFRACTIONr_bond_other_d0.0020.022040
X-RAY DIFFRACTIONr_angle_refined_deg2.4381.963110
X-RAY DIFFRACTIONr_angle_other_deg1.263.0074741
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3715282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15423.178107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37215369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7171519
X-RAY DIFFRACTIONr_chiral_restr0.1620.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212537
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02479
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_it2.7523.2141104
X-RAY DIFFRACTIONr_mcbond_other2.7533.2111103
X-RAY DIFFRACTIONr_mcangle_it3.7284.7891382
X-RAY DIFFRACTIONr_mcangle_other3.7274.7931383
X-RAY DIFFRACTIONr_scbond_it4.3093.7381177
X-RAY DIFFRACTIONr_scbond_other4.3133.7391175
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4285.4211723
X-RAY DIFFRACTIONr_long_range_B_refined7.85638.8332542
X-RAY DIFFRACTIONr_long_range_B_other7.85438.8252543
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 96 -
Rwork0.283 1817 -
obs--99.84 %
Refinement TLS params.Method: refined / Origin x: 11.7105 Å / Origin y: 22.3351 Å / Origin z: -15.0972 Å
111213212223313233
T0.0062 Å2-0.0109 Å20.0017 Å2-0.0551 Å2-0.0102 Å2--0.0148 Å2
L0.3641 °20.1601 °2-0.439 °2-0.3592 °2-0.1169 °2--0.5823 °2
S0.0226 Å °-0.0179 Å °0.0039 Å °-0.0142 Å °-0.0337 Å °-0.0136 Å °-0.0209 Å °-0.0242 Å °0.0111 Å °

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