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- PDB-7u59: Crystal Structure of Danio rerio Histone Deacetylase 10 in Comple... -

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Basic information

Entry
Database: PDB / ID: 7u59
TitleCrystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Piperidine-4-hydroxamic acid Inhibitor
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 / regulation of tubulin deacetylation / 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-LDI / PHOSPHATE ION / Polyamine deacetylase HDAC10
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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: Chembiochem / Year: 2022
Title: First Fluorescent Acetylspermidine Deacetylation Assay for HDAC10 Identifies Selective Inhibitors with Cellular Target Engagement.
Authors: Herp, D. / Ridinger, J. / Robaa, D. / Shinsky, S.A. / Schmidtkunz, K. / Yesiloglu, T.Z. / Bayer, T. / Steimbach, R.R. / Herbst-Gervasoni, C.J. / Merz, A. / Romier, C. / Sehr, P. / Gunkel, N. ...Authors: Herp, D. / Ridinger, J. / Robaa, D. / Shinsky, S.A. / Schmidtkunz, K. / Yesiloglu, T.Z. / Bayer, T. / Steimbach, R.R. / Herbst-Gervasoni, C.J. / Merz, A. / Romier, C. / Sehr, P. / Gunkel, N. / Miller, A.K. / Christianson, D.W. / Oehme, I. / Sippl, W. / Jung, M.
History
DepositionMar 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 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

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Assembly

Deposited unit
A: Polyamine deacetylase HDAC10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,98412
Polymers75,0691
Non-polymers91511
Water4,756264
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)80.849, 80.849, 247.467
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: 75068.641 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 , 7 types, 275 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-LDI / 1-[2-(benzylamino)ethyl]-N-hydroxypiperidine-4-carboxamide


Mass: 277.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


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


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


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


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


Mass: 18.015 Da / Num. of mol.: 264 / 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: 3.11 Å3/Da / Density % sol: 60.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL HDAC10, 2 mM inhibitor, 1:1000 trypsin:HDAC10, 0.100 M Sodium Phosphate Monobasic, 0.100 M Sodium Phosphate Dibasic, and 20% (w/v) PEG3350. Microseed crystals of HDAC10-Tubastatin A ...Details: 10 mg/mL HDAC10, 2 mM inhibitor, 1:1000 trypsin:HDAC10, 0.100 M Sodium Phosphate Monobasic, 0.100 M Sodium Phosphate Dibasic, and 20% (w/v) PEG3350. Microseed crystals of HDAC10-Tubastatin A were added to the drop as well

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.18→70.02 Å / Num. obs: 99611 / % possible obs: 99.8 % / Redundancy: 7 % / Biso Wilson estimate: 37.67 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.078 / Net I/σ(I): 8.6
Reflection shellResolution: 2.18→2.25 Å / Rmerge(I) obs: 1.213 / Mean I/σ(I) obs: 2 / Num. unique obs: 4286 / CC1/2: 0.664 / Rpim(I) all: 0.709

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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: 2.18→60.94 Å / SU ML: 0.2433 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.9619
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2098 2558 5.13 %
Rwork0.1791 47278 -
obs0.1808 49836 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.68 Å2
Refinement stepCycle: LAST / Resolution: 2.18→60.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4832 0 51 264 5147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00735018
X-RAY DIFFRACTIONf_angle_d0.92166844
X-RAY DIFFRACTIONf_chiral_restr0.0518791
X-RAY DIFFRACTIONf_plane_restr0.0061878
X-RAY DIFFRACTIONf_dihedral_angle_d9.06484041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.220.24411220.23312613X-RAY DIFFRACTION99.85
2.22-2.270.29971250.24562568X-RAY DIFFRACTION99.52
2.27-2.320.26631360.23162601X-RAY DIFFRACTION99.89
2.32-2.370.26671300.21912629X-RAY DIFFRACTION99.82
2.37-2.430.29411180.21052598X-RAY DIFFRACTION99.82
2.43-2.50.26841550.20682559X-RAY DIFFRACTION99.67
2.5-2.570.23451380.20272588X-RAY DIFFRACTION99.85
2.57-2.650.26541430.20372609X-RAY DIFFRACTION99.78
2.65-2.750.28851270.19922649X-RAY DIFFRACTION99.93
2.75-2.860.23231170.20912634X-RAY DIFFRACTION99.93
2.86-2.990.25591340.20522620X-RAY DIFFRACTION99.24
2.99-3.140.24531360.20422590X-RAY DIFFRACTION99.27
3.14-3.340.2361700.18792631X-RAY DIFFRACTION99.82
3.34-3.60.24431480.17112613X-RAY DIFFRACTION99.86
3.6-3.960.17361950.15642594X-RAY DIFFRACTION99.82
3.96-4.530.17331290.13932706X-RAY DIFFRACTION99.89
4.53-5.710.16361750.15042655X-RAY DIFFRACTION99.05
5.71-60.940.16041600.16042821X-RAY DIFFRACTION98.32

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