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- PDB-8d9a: Crystal Structure of Danio rerio histone deacetylase 6 catalytic ... -

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Basic information

Entry
Database: PDB / ID: 8d9a
TitleCrystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with fluorinated inhibitor 8
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 / 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
: / 2,3,5-trifluoro-N-hydroxybenzamide / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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)81,24010
Polymers80,5712
Non-polymers6698
Water7,800433
1
A: 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
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)75.035, 92.044, 96.200
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-QHO / 2,3,5-trifluoro-N-hydroxybenzamide


Mass: 191.107 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H4F3NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 2.06 Å3/Da / Density % sol: 40.34 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop
Details: 10mg/mL HDAC6 Protein, 0.09 M Bis-tris (pH 6.0), 0.18 M KSCN, 18% PEG 3350, 0.3% ethanol

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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: Dec 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→96.2 Å / Num. obs: 447487 / % possible obs: 99.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 19.1 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.8
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 21506 / CC1/2: 0.902

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Processing

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

5eem


Resolution: 1.75→66.51 Å / SU ML: 0.2017 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.855
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2172 1998 2.95 %
Rwork0.1834 65709 -
obs0.1844 67707 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.26 Å2
Refinement stepCycle: LAST / Resolution: 1.75→66.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5446 0 32 433 5911
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00675665
X-RAY DIFFRACTIONf_angle_d0.89917719
X-RAY DIFFRACTIONf_chiral_restr0.0552849
X-RAY DIFFRACTIONf_plane_restr0.00861012
X-RAY DIFFRACTIONf_dihedral_angle_d23.5128789
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.27021300.2564408X-RAY DIFFRACTION94.84
1.79-1.840.26331420.23034653X-RAY DIFFRACTION99.61
1.84-1.890.2561280.21574648X-RAY DIFFRACTION99.56
1.89-1.950.23991580.20274642X-RAY DIFFRACTION99.73
1.95-2.020.24751430.19564675X-RAY DIFFRACTION99.83
2.02-2.110.25721370.19554664X-RAY DIFFRACTION99.67
2.11-2.20.24591390.20264668X-RAY DIFFRACTION99.28
2.2-2.320.23411480.1914677X-RAY DIFFRACTION99.73
2.32-2.460.22481370.18464696X-RAY DIFFRACTION99.75
2.46-2.650.2331460.18754703X-RAY DIFFRACTION99.79
2.65-2.920.21971450.19574736X-RAY DIFFRACTION99.84
2.92-3.340.23961440.19064746X-RAY DIFFRACTION99.78
3.34-4.210.16031490.15664817X-RAY DIFFRACTION99.8
4.21-66.510.18651520.15264976X-RAY DIFFRACTION99.61

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