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- PDB-6wdv: Crystal Structure of Danio rerio Histone Deacetylase 10 in Comple... -

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Basic information

Entry
Database: PDB / ID: 6wdv
TitleCrystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Dimethylaminomethylindole Phenylhydroxamate Inhibitor
ComponentsPolyamine deacetylase HDAC10
KeywordsHydrolase/Hydrolase Inhibitor / Histone Deacetylase / Hydrolase-Hydrolase Inhibitor complex
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 ...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 / macroautophagy / negative regulation of transcription by RNA polymerase II / 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
: / PHOSPHATE ION / Chem-TWM / Polyamine deacetylase HDAC10
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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: Acs Chem.Biol. / Year: 2020
Title: Structural Basis for the Selective Inhibition of HDAC10, the Cytosolic Polyamine Deacetylase.
Authors: Herbst-Gervasoni, C.J. / Steimbach, R.R. / Morgen, M. / Miller, A.K. / Christianson, D.W.
History
DepositionApr 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Sep 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: 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

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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)75,7137
Polymers75,0561
Non-polymers6576
Water3,027168
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-13 kcal/mol
Surface area23600 Å2
Unit cell
Length a, b, c (Å)80.670, 80.670, 246.842
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 , 5 types, 174 molecules

#2: Chemical ChemComp-TWM / 4-({3-[(dimethylamino)methyl]-1H-indol-1-yl}methyl)-N-hydroxybenzamide


Mass: 323.389 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL HDAC10, 2 mM inhibitor, 1:1000 trypsin:HDAC10, 0.135 M sodium phosphate monobasic, 0.045 M sodium phosphate dibasic, 18% PEG3350 (w/v), and 0.5% (w/v) n-dodecyl-N,N-dimethylamine-N-oxide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.4→69.86 Å / Num. obs: 37432 / % possible obs: 100 % / Redundancy: 9 % / Biso Wilson estimate: 46.13 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.068 / Net I/σ(I): 9.7
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 1.111 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3654 / CC1/2: 0.557 / Rpim(I) all: 0.603

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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: 2.4→69.86 Å / SU ML: 0.3213 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3244
RfactorNum. reflection% reflection
Rfree0.2267 1938 5.18 %
Rwork0.1813 --
obs0.1837 37428 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 52.7 Å2
Refinement stepCycle: LAST / Resolution: 2.4→69.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4830 0 37 168 5035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00725008
X-RAY DIFFRACTIONf_angle_d0.92976829
X-RAY DIFFRACTIONf_chiral_restr0.0509779
X-RAY DIFFRACTIONf_plane_restr0.0059882
X-RAY DIFFRACTIONf_dihedral_angle_d9.87394044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.31791290.26782481X-RAY DIFFRACTION100
2.46-2.530.33291570.25032492X-RAY DIFFRACTION100
2.53-2.60.28981150.24142519X-RAY DIFFRACTION100
2.6-2.680.32661390.23842486X-RAY DIFFRACTION100
2.68-2.780.30261440.21952488X-RAY DIFFRACTION99.96
2.78-2.890.2561250.21082512X-RAY DIFFRACTION99.96
2.89-3.020.26431180.21632514X-RAY DIFFRACTION100
3.02-3.180.25691330.20952516X-RAY DIFFRACTION100
3.18-3.380.28581400.20742536X-RAY DIFFRACTION99.96
3.38-3.640.23411660.18392483X-RAY DIFFRACTION99.85
3.64-4.010.19411270.15652570X-RAY DIFFRACTION100
4.01-4.590.18641680.13962516X-RAY DIFFRACTION99.93
4.59-5.780.17671450.14242628X-RAY DIFFRACTION99.96
5.78-69.860.19161320.17092749X-RAY DIFFRACTION99.79

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