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- PDB-8d99: Crystal Structure of Danio rerio histone deacetylase 6 catalytic ... -

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Basic information

Entry
Database: PDB / ID: 8d99
TitleCrystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with fluorinated inhibitor 7
ComponentsHdac6 protein
KeywordsHYDROLASE/INHIBITOR / Hydrolase / histone deacetylase / inhibitor / metallohydrolase / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / regulation of tubulin deacetylation / histone deacetylase activity / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation / epigenetic regulation of gene expression ...tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / regulation of tubulin deacetylation / 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
: / 2,3,6-trifluoro-N-hydroxybenzamide / Hdac6 protein
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsWatson, P.R. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM49758 United States
CitationJournal: Biochemistry / Year: 2022
Title: Aromatic Ring Fluorination Patterns Modulate Inhibitory Potency of Fluorophenylhydroxamates Complexed with Histone Deacetylase 6.
Authors: Watson, P.R. / Bai, P. / Wang, C. / Cragin, A.D. / Hooker, J.M. / Christianson, D.W.
History
DepositionJun 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hdac6 protein
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0499
Polymers80,5712
Non-polymers4787
Water4,378243
1
A: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4294
Polymers40,2851
Non-polymers1443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6205
Polymers40,2851
Non-polymers3354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.900, 95.576, 96.852
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Hdac6 protein / Histone Deacetylase 6


Mass: 40285.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Production host: Escherichia coli (E. coli) / References: UniProt: A7YT55
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-QH7 / 2,3,6-trifluoro-N-hydroxybenzamide


Mass: 191.107 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H4F3NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL HDAC6 0.09 M Bis-tris (pH 6.0), 0.18 M KSCN, 18% PEG 3350, 0.4% tert-butanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.79→95.58 Å / Num. obs: 434665 / % possible obs: 99.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 16.66 Å2 / CC1/2: 0.998 / Net I/σ(I): 16
Reflection shellResolution: 1.79→1.82 Å / Num. unique obs: 21816 / CC1/2: 0.958

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 5EEM

5eem


Resolution: 1.79→59.25 Å / SU ML: 0.2022 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.299
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2195 1986 3.01 %
Rwork0.1914 64039 -
obs0.1923 66025 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.22 Å2
Refinement stepCycle: LAST / Resolution: 1.79→59.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5455 0 19 243 5717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00665625
X-RAY DIFFRACTIONf_angle_d0.87337652
X-RAY DIFFRACTIONf_chiral_restr0.0532843
X-RAY DIFFRACTIONf_plane_restr0.00941000
X-RAY DIFFRACTIONf_dihedral_angle_d20.7196775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.830.30211300.24834273X-RAY DIFFRACTION94.2
1.83-1.880.25841390.21324509X-RAY DIFFRACTION99.27
1.88-1.940.21511400.18314550X-RAY DIFFRACTION99.6
1.94-20.23241410.1784522X-RAY DIFFRACTION99.38
2-2.070.24031390.17894565X-RAY DIFFRACTION99.51
2.07-2.150.23571460.18114545X-RAY DIFFRACTION99.41
2.15-2.250.21561380.18554558X-RAY DIFFRACTION99.28
2.25-2.370.22491410.1894541X-RAY DIFFRACTION99.53
2.37-2.520.22521460.18574591X-RAY DIFFRACTION99.62
2.52-2.710.2211420.18624590X-RAY DIFFRACTION99.56
2.71-2.980.21161460.19724618X-RAY DIFFRACTION99.67
2.98-3.420.21741420.20564635X-RAY DIFFRACTION99.69
3.42-4.30.19721470.18744681X-RAY DIFFRACTION99.67
4.3-59.250.20911490.18824861X-RAY DIFFRACTION99.39

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