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- PDB-6wyp: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -

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Basic information

Entry
Database: PDB / ID: 6wyp
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) K330L mutant complexed with SAHA-BPyne
ComponentsHistone deacetylase 6
KeywordsHYDROLASE / Histone Deacetylase / metalloprotein
Function / homology
Function and homology information


Aggrephagy / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / histone deacetylase activity / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation / epigenetic regulation of gene expression ...Aggrephagy / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / histone deacetylase activity / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation / epigenetic regulation of gene expression / angiogenesis / zinc ion binding
Similarity search - Function
Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
: / Chem-UFS / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.40006356531 Å
AuthorsOsko, J.D. / 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: Acta Crystallogr.,Sect.F / Year: 2020
Title: Binding of inhibitors to active-site mutants of CD1, the enigmatic catalytic domain of histone deacetylase 6.
Authors: Osko, J.D. / Christianson, D.W.
History
DepositionMay 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 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: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6585
Polymers42,0371
Non-polymers6214
Water84747
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint0 kcal/mol
Surface area12540 Å2
Unit cell
Length a, b, c (Å)66.029, 95.170, 119.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Histone deacetylase 6


Mass: 42036.602 Da / Num. of mol.: 1 / Mutation: K330L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Production host: Escherichia coli (E. coli) / References: UniProt: F8W4B7
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-UFS / N~1~-(4-{4-[(hex-5-ynoyl)amino]benzene-1-carbonyl}phenyl)-N~8~-hydroxyoctanediamide


Mass: 477.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H31N3O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL HDAC6 Protein 0.2 M Potassium Sodium Tartrate Tetrahydrate 20% PEG 3350 1:1 ratio protein to precipitant solution

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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: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.4→54.26 Å / Num. obs: 15104 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 45.9586092758 Å2 / CC1/2: 0.971 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.119 / Net I/σ(I): 4.8
Reflection shellResolution: 2.4→2.486 Å / Rmerge(I) obs: 0.817 / Num. unique obs: 1483 / CC1/2: 0.618 / Rpim(I) all: 0.507

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 5EEF

5eef


Resolution: 2.40006356531→54.25087491 Å / SU ML: 0.249125312227 / Cross valid method: FREE R-VALUE / σ(F): 1.33784508885 / Phase error: 25.3867738361
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.242720440807 729 4.8268555916 %
Rwork0.203136372799 14374 -
obs0.205098738814 15103 99.9338318004 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.1448075816 Å2
Refinement stepCycle: LAST / Resolution: 2.40006356531→54.25087491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2688 0 38 47 2773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002833084460572826
X-RAY DIFFRACTIONf_angle_d0.578722505063844
X-RAY DIFFRACTIONf_chiral_restr0.0423714255156425
X-RAY DIFFRACTIONf_plane_restr0.00348803146209499
X-RAY DIFFRACTIONf_dihedral_angle_d15.03592857081641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.58540.2822323320051460.2551669709562818X-RAY DIFFRACTION99.8652291105
2.5854-2.84550.318524593621290.2630551310362844X-RAY DIFFRACTION100
2.8455-3.25720.3288526188761610.2430767562932856X-RAY DIFFRACTION99.9668654738
3.2572-4.10360.2677909874731390.2054694403582872X-RAY DIFFRACTION100
4.1036-54.250.1771150789251540.163573786032984X-RAY DIFFRACTION99.8726925525

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