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

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Basic information

Entry
Database: PDB / ID: 7sgk
TitleCrystal Structure of Danio rerio Histone Deacetylase 10 in Complex with DKFZ-728
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-9A9 / : / PHOSPHATE ION / Polyamine deacetylase HDAC10
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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

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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
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.548, 80.548, 243.350
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, 252 molecules

#2: Chemical ChemComp-9A9 / N-(2-{[4-(hydroxyamino)-4-oxobutyl](methyl)amino}ethyl)benzamide


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.: 244 / 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: 3.04 Å3/Da / Density % sol: 59.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL HDAC10, 2 mM DKFZ-728, 1:1000 trypsin:HDAC10, 0.192 M Sodium Phosphate Monobasic, 0.008 M Sodium Phosphate Dibasic, 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: 2.2→69.76 Å / Num. obs: 47515 / % possible obs: 99.8 % / Redundancy: 9.1 % / Biso Wilson estimate: 39.49 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.072 / Net I/σ(I): 9.4
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 1.322 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4052 / CC1/2: 0.667 / Rpim(I) all: 0.653

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TD7

5td7


Resolution: 2.2→69.76 Å / SU ML: 0.3014 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.7023 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2429 2395 5.05 %
Rwork0.1953 45034 -
obs0.1977 47429 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.56 Å2
Refinement stepCycle: LAST / Resolution: 2.2→69.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4837 0 39 244 5120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00735016
X-RAY DIFFRACTIONf_angle_d0.92056840
X-RAY DIFFRACTIONf_chiral_restr0.051785
X-RAY DIFFRACTIONf_plane_restr0.006882
X-RAY DIFFRACTIONf_dihedral_angle_d9.59594056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.35981450.31252644X-RAY DIFFRACTION100
2.25-2.290.33491660.29272561X-RAY DIFFRACTION99.96
2.29-2.350.35681540.27742566X-RAY DIFFRACTION100
2.35-2.410.27961220.25512637X-RAY DIFFRACTION99.93
2.41-2.470.29631160.24452633X-RAY DIFFRACTION100
2.47-2.540.28451450.23842614X-RAY DIFFRACTION100
2.54-2.630.30041580.23432608X-RAY DIFFRACTION100
2.63-2.720.26961290.22282635X-RAY DIFFRACTION99.78
2.72-2.830.31011270.21532636X-RAY DIFFRACTION99.96
2.83-2.960.28251220.2122664X-RAY DIFFRACTION100
2.96-3.110.25141440.21162636X-RAY DIFFRACTION99.93
3.11-3.310.26271700.2072617X-RAY DIFFRACTION99.89
3.31-3.560.271540.19062635X-RAY DIFFRACTION99.54
3.56-3.920.23831440.17672666X-RAY DIFFRACTION99.96
3.92-4.490.17761400.15292714X-RAY DIFFRACTION99.86
4.49-5.660.18961110.15642715X-RAY DIFFRACTION98.54
5.66-69.760.19791480.17732853X-RAY DIFFRACTION98.49

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