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

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Basic information

Entry
Database: PDB / ID: 6wdx
TitleCrystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Hydroxyethylindole Phenylhydroxamate Inhibitor
ComponentsPolyamine deacetylase HDAC10
KeywordsHydolase/Hydrolase Inhibitor / Histone Deacetylase / Hydolase-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 / 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
: / PHOSPHATE ION / Chem-TWS / Polyamine deacetylase HDAC10
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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
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)75,7958
Polymers75,0561
Non-polymers7397
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-19 kcal/mol
Surface area22890 Å2
Unit cell
Length a, b, c (Å)80.440, 80.440, 243.891
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, 94 molecules

#2: Chemical ChemComp-TWS / N-hydroxy-4-{[3-(2-hydroxyethyl)-1H-indol-1-yl]methyl}benzamide


Mass: 310.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N2O3 / 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#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


Mass: 18.015 Da / Num. of mol.: 87 / 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: 3.24 Å3/Da / Density % sol: 62.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL HDAC10, 4 mM inhibitor, 1:1000 trypsin:HDAC10, 0.175 M sodium phosphate monobasic, 0.025 M sodium phosphate dibasic, and 20% PEG3350 (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.65→69.66 Å / Num. obs: 27467 / % possible obs: 99.9 % / Redundancy: 9.8 % / Biso Wilson estimate: 50.48 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.1 / Net I/σ(I): 8.1
Reflection shellResolution: 2.65→2.78 Å / Rmerge(I) obs: 1.066 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2673 / CC1/2: 0.533 / Rpim(I) all: 0.524

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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: 2.65→66.98 Å / SU ML: 0.3608 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.2065
RfactorNum. reflection% reflection
Rfree0.2549 1405 5.12 %
Rwork0.198 --
obs0.2009 27464 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 55.96 Å2
Refinement stepCycle: LAST / Resolution: 2.65→66.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4717 0 41 87 4845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084877
X-RAY DIFFRACTIONf_angle_d1.00946653
X-RAY DIFFRACTIONf_chiral_restr0.0514761
X-RAY DIFFRACTIONf_plane_restr0.0061860
X-RAY DIFFRACTIONf_dihedral_angle_d6.173885
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.740.35471340.28342539X-RAY DIFFRACTION99.59
2.74-2.850.31271230.26162583X-RAY DIFFRACTION99.74
2.85-2.980.2881440.24472566X-RAY DIFFRACTION99.67
2.98-3.140.33321200.23322548X-RAY DIFFRACTION99.63
3.14-3.340.2891440.23062602X-RAY DIFFRACTION99.78
3.34-3.60.25921560.20032538X-RAY DIFFRACTION99.93
3.6-3.960.24921530.17932593X-RAY DIFFRACTION99.93
3.96-4.530.23511380.15252624X-RAY DIFFRACTION99.89
4.53-5.710.20951450.16762660X-RAY DIFFRACTION100
5.71-66.980.2321480.22806X-RAY DIFFRACTION99.86

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