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

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Basic information

Entry
Database: PDB / ID: 6wbq
TitleCrystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Tubastatin A
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-N9W / PHOSPHATE ION / Polyamine deacetylase HDAC10
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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: 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
DepositionMar 27, 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 ...citation / citation_author / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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 1.4Oct 30, 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)76,13013
Polymers75,0561
Non-polymers1,07412
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-7 kcal/mol
Surface area23260 Å2
Unit cell
Length a, b, c (Å)80.630, 80.630, 246.811
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, 206 molecules

#2: Chemical ChemComp-N9W / 4-[(2-methyl-3,4-dihydro-1~{H}-pyrido[4,3-b]indol-5-yl)methyl]-~{N}-oxidanyl-benzamide


Mass: 335.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 3.09 Å3/Da / Density % sol: 60.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL HDAC10, 2 mM inhibitor, 1:1000 trypsin:HDAC10, 0.158 M sodium phosphate monobasic, 0.023 M sodium phosphate dibasic, 18% PEG3350 (w/v), and 0.01 M Taurine

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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→53.24 Å / Num. obs: 63801 / % possible obs: 99.7 % / Redundancy: 9.2 % / Biso Wilson estimate: 35.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.046 / Net I/σ(I): 13.5
Reflection shellResolution: 2→2.072 Å / Rmerge(I) obs: 1.32 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 6329 / CC1/2: 0.638 / Rpim(I) all: 0.668

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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→53.24 Å / SU ML: 0.2445 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.4826
RfactorNum. reflection% reflection
Rfree0.2351 3185 4.99 %
Rwork0.1994 --
obs0.2011 63789 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.14 Å2
Refinement stepCycle: LAST / Resolution: 2→53.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4816 0 63 194 5073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00725020
X-RAY DIFFRACTIONf_angle_d0.88686840
X-RAY DIFFRACTIONf_chiral_restr0.0514780
X-RAY DIFFRACTIONf_plane_restr0.0058879
X-RAY DIFFRACTIONf_dihedral_angle_d8.95464055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.32581300.30552599X-RAY DIFFRACTION99.96
2.03-2.060.28561330.29422621X-RAY DIFFRACTION100
2.06-2.10.32011480.28112555X-RAY DIFFRACTION99.93
2.1-2.130.3211000.27362664X-RAY DIFFRACTION100
2.13-2.170.31571460.25652596X-RAY DIFFRACTION100
2.17-2.210.25731580.25062540X-RAY DIFFRACTION99.85
2.21-2.260.27561510.24092589X-RAY DIFFRACTION98.63
2.26-2.310.25841480.23112593X-RAY DIFFRACTION99.28
2.31-2.360.26721400.21992617X-RAY DIFFRACTION100
2.36-2.420.27771320.22062597X-RAY DIFFRACTION100
2.42-2.480.26531400.22612605X-RAY DIFFRACTION100
2.48-2.560.25571370.2242611X-RAY DIFFRACTION99.96
2.56-2.640.23461340.22422638X-RAY DIFFRACTION99.96
2.64-2.730.26021320.2172615X-RAY DIFFRACTION99.24
2.73-2.840.26041640.21812606X-RAY DIFFRACTION98.82
2.84-2.970.28381320.21462627X-RAY DIFFRACTION100
2.97-3.130.22551460.2112645X-RAY DIFFRACTION99.96
3.13-3.330.22791530.21182650X-RAY DIFFRACTION99.93
3.33-3.580.22151140.19192648X-RAY DIFFRACTION99.21
3.58-3.940.20211370.17612665X-RAY DIFFRACTION99.64
3.94-4.510.19681370.15862706X-RAY DIFFRACTION99.82
4.51-5.690.19241410.15912718X-RAY DIFFRACTION99.34
5.69-53.240.22631320.17582899X-RAY DIFFRACTION99.67

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