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

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Basic information

Entry
Database: PDB / ID: 6wdy
TitleCrystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Indole 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 / 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
: / PHOSPHATE ION / N-hydroxy-4-[(1H-indol-1-yl)methyl]benzamide / 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

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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)75,8139
Polymers75,0561
Non-polymers7578
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-13 kcal/mol
Surface area23610 Å2
Unit cell
Length a, b, c (Å)80.670, 80.670, 243.980
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, 97 molecules

#2: Chemical ChemComp-TWP / N-hydroxy-4-[(1H-indol-1-yl)methyl]benzamide


Mass: 266.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 3.05 Å3/Da / Density % sol: 59.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL HDAC10, 2 mM inhibitor, 1:1000 trypsin:HDAC10, 0.152 M potassium phosphate monobasic, 0.048 M potassium 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: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / 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: 2.65→69.86 Å / Num. obs: 27673 / % possible obs: 100 % / Redundancy: 9 % / Biso Wilson estimate: 49.12 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.095 / Net I/σ(I): 8.4
Reflection shellResolution: 2.65→2.78 Å / Rmerge(I) obs: 1.123 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2716 / CC1/2: 0.651 / Rpim(I) all: 0.57

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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→69.86 Å / SU ML: 0.3446 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.128 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2552 1411 5.1 %
Rwork0.1902 26259 -
obs0.1935 27670 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.45 Å2
Refinement stepCycle: LAST / Resolution: 2.65→69.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4789 0 42 89 4920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00834967
X-RAY DIFFRACTIONf_angle_d1.01726774
X-RAY DIFFRACTIONf_chiral_restr0.054775
X-RAY DIFFRACTIONf_plane_restr0.0064873
X-RAY DIFFRACTIONf_dihedral_angle_d22.84371757
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.740.32431280.24942588X-RAY DIFFRACTION100
2.74-2.850.31631330.2392589X-RAY DIFFRACTION100
2.85-2.980.29571400.2322580X-RAY DIFFRACTION99.93
2.98-3.140.31441220.23172592X-RAY DIFFRACTION100
3.14-3.340.2971470.22542603X-RAY DIFFRACTION99.96
3.34-3.60.25561530.19362563X-RAY DIFFRACTION99.96
3.6-3.960.24321580.17842606X-RAY DIFFRACTION100
3.96-4.530.21891350.15182649X-RAY DIFFRACTION100
4.53-5.710.20691480.1562666X-RAY DIFFRACTION99.89
5.71-69.860.26281470.19222823X-RAY DIFFRACTION99.8

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