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- PDB-7sgi: Crystal Structure of Danio rerio Histone Deacetylase 10 in Comple... -

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Basic information

Entry
Database: PDB / ID: 7sgi
TitleCrystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Inhibitor 14
ComponentsPolyamine deacetylase HDAC10
KeywordsHYDROLASE / Histone Deacetylase
Function / homology
Function and homology information


polyamine deacetylation / spermidine deacetylation / HDACs deacetylate histones / acetylspermidine deacetylase / acetylspermidine deacetylase activity / acetylputrescine deacetylase / acetylputrescine deacetylase activity / deacetylase activity / homologous recombination / swimming behavior ...polyamine deacetylation / spermidine deacetylation / HDACs deacetylate histones / acetylspermidine deacetylase / acetylspermidine deacetylase activity / acetylputrescine deacetylase / acetylputrescine deacetylase activity / deacetylase activity / homologous recombination / swimming behavior / epigenetic regulation of gene expression / macroautophagy / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
: / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily
Similarity search - Domain/homology
Chem-9DL / : / PHOSPHATE ION / Polyamine deacetylase HDAC10
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHerbst-Gervasoni, C.J. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM49758 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Aza-SAHA Derivatives Are Selective Histone Deacetylase 10 Chemical Probes That Inhibit Polyamine Deacetylation and Phenocopy HDAC10 Knockout.
Authors: Steimbach, R.R. / Herbst-Gervasoni, C.J. / Lechner, S. / Stewart, T.M. / Klinke, G. / Ridinger, J. / Geraldy, M.N.E. / Tihanyi, G. / Foley, J.R. / Uhrig, U. / Kuster, B. / Poschet, G. / ...Authors: Steimbach, R.R. / Herbst-Gervasoni, C.J. / Lechner, S. / Stewart, T.M. / Klinke, G. / Ridinger, J. / Geraldy, M.N.E. / Tihanyi, G. / Foley, J.R. / Uhrig, U. / Kuster, B. / Poschet, G. / Casero Jr., R.A. / Medard, G. / Oehme, I. / Christianson, D.W. / Gunkel, N. / Miller, A.K.
History
DepositionOct 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyamine deacetylase HDAC10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7869
Polymers75,0561
Non-polymers7318
Water4,306239
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.500, 80.500, 246.632
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Polyamine deacetylase HDAC10 / Histone deacetylase 10


Mass: 75055.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac10 / Production host: Escherichia coli (E. coli)
References: UniProt: F1QCV2, acetylspermidine deacetylase, acetylputrescine deacetylase

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Non-polymers , 6 types, 247 molecules

#2: Chemical ChemComp-9DL / 5-[(2-anilino-2-oxoethyl)(methyl)amino]-N-hydroxypentanamide


Mass: 279.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.07 Å3/Da / Density % sol: 59.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL HDAC10, 2 mM Inhibitor 14, 1:1000 trypsin:HDAC10, 0.131 M Sodium Phosphate Monobasic, 0.044 M Sodium Phosphate Dibasic, 3% (v/v) glycerol, and 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.15→69.71 Å / Num. obs: 51497 / % possible obs: 100 % / Redundancy: 9.3 % / Biso Wilson estimate: 34.1 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.068 / Net I/σ(I): 10.8
Reflection shellResolution: 2.15→2.21 Å / Rmerge(I) obs: 1.168 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4158 / CC1/2: 0.574 / Rpim(I) all: 0.631

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TD7

5td7


Resolution: 2.15→69.71 Å / SU ML: 0.2675 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3783
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2223 2671 5.19 %
Rwork0.1899 48826 -
obs0.1916 51497 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.33 Å2
Refinement stepCycle: LAST / Resolution: 2.15→69.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4814 0 39 239 5092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00734986
X-RAY DIFFRACTIONf_angle_d0.8986795
X-RAY DIFFRACTIONf_chiral_restr0.0506780
X-RAY DIFFRACTIONf_plane_restr0.0061874
X-RAY DIFFRACTIONf_dihedral_angle_d23.30351775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.190.32951350.28042527X-RAY DIFFRACTION99.85
2.19-2.230.28711210.27082570X-RAY DIFFRACTION100
2.23-2.280.30821670.24342480X-RAY DIFFRACTION100
2.28-2.330.29381520.2332522X-RAY DIFFRACTION100
2.33-2.380.25871510.22362518X-RAY DIFFRACTION100
2.38-2.440.26661310.21982553X-RAY DIFFRACTION99.96
2.44-2.510.27091410.21672532X-RAY DIFFRACTION100
2.51-2.580.29731120.21752541X-RAY DIFFRACTION99.92
2.58-2.660.26211380.20542547X-RAY DIFFRACTION100
2.66-2.760.2761480.20592547X-RAY DIFFRACTION100
2.76-2.870.25291360.20392550X-RAY DIFFRACTION100
2.87-30.24831230.20872589X-RAY DIFFRACTION100
3-3.160.25491380.20852547X-RAY DIFFRACTION100
3.16-3.350.23191320.20512601X-RAY DIFFRACTION100
3.35-3.610.23161120.1822582X-RAY DIFFRACTION99.93
3.61-3.980.19731590.16392595X-RAY DIFFRACTION100
3.98-4.550.17811710.1472582X-RAY DIFFRACTION100
4.55-5.740.16081290.15032677X-RAY DIFFRACTION100
5.74-69.710.18351750.1822766X-RAY DIFFRACTION99.59

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