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- PDB-9egu: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -

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Basic information

Entry
Database: PDB / ID: 9egu
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with TO-599
ComponentsHdac6 protein
KeywordsMETAL BINDING PROTEIN / potassium ion binding / alkali metal ion binding / ion binding / cation binding / metal ion binding / catalytic activity / hydrolase activity / deacetylase activity / protein deacetylase activity / acting on a protein / acting on carbon-nitrogen (but not peptide) bonds / in linear amides / tubulin deacetylase activity / zinc ion binding / transition metal ion binding
Function / homology
Function and homology information


swimming behavior / tubulin deacetylase activity / 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 ...swimming behavior / tubulin deacetylase activity / 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
: / : / Hdac6 protein
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsErdogan, F. / Seo, H.-S. / Dhe-Paganon, S.
Funding support Canada, 5items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2014-05767 Canada
Canadian Institutes of Health Research (CIHR)MOP-130424 Canada
Canada Research Chairs950-232042 Canada
Ontario Research Fund34876 Canada
Canada Foundation for Innovation33536 Canada
CitationJournal: To Be Published
Title: Bisected Cap Group Modifications Provides Basis for Improved Pharmacokinetics of HDAC Inhibitors
Authors: Olaoye, O. / Erdogan, F. / Gunning, P.T.
History
DepositionNov 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,4668
Polymers79,4502
Non-polymers1,0166
Water10,160564
1
A: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2334
Polymers39,7251
Non-polymers5083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2334
Polymers39,7251
Non-polymers5083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.790, 91.190, 96.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hdac6 protein / Histone Deacetylase 6


Mass: 39724.973 Da / Num. of mol.: 2 / Fragment: catalytic domain 2 (UNP residues 290-646)
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-A1BH9 / N-hydroxy-4-({[(pyridin-3-yl)methyl](thiophene-3-sulfonyl)amino}methyl)benzamide


Mass: 403.475 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H17N3O4S2 / 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.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 40.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 4K, 0.2M NH4 Acet. 0.1M Na Citrate 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.27→91.19 Å / Num. obs: 162298 / % possible obs: 93.7 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.037 / Rrim(I) all: 0.097 / Net I/σ(I): 8.9 / Num. measured all: 1079785
Reflection shellResolution: 1.27→1.29 Å / % possible obs: 60.6 % / Redundancy: 4.9 % / Rmerge(I) obs: 2.127 / Num. measured all: 25511 / Num. unique obs: 5163 / CC1/2: 0.313 / Rpim(I) all: 1.027 / Rrim(I) all: 2.377 / Net I/σ(I) obs: 0.6

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
xia2data scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.27→59.036 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2212 8136 5.03 %
Rwork0.208 --
obs0.2086 161851 93.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.27→59.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5566 0 58 564 6188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055878
X-RAY DIFFRACTIONf_angle_d0.8037988
X-RAY DIFFRACTIONf_dihedral_angle_d3.8093388
X-RAY DIFFRACTIONf_chiral_restr0.076856
X-RAY DIFFRACTIONf_plane_restr0.0051050
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.28440.41891410.40493193X-RAY DIFFRACTION58
1.2844-1.29950.40171900.38153430X-RAY DIFFRACTION63
1.2995-1.31540.40851950.37613731X-RAY DIFFRACTION69
1.3154-1.33210.36722040.36744158X-RAY DIFFRACTION77
1.3321-1.34960.35222380.36324665X-RAY DIFFRACTION85
1.3496-1.36810.38582940.34525054X-RAY DIFFRACTION93
1.3681-1.38760.32952520.3255160X-RAY DIFFRACTION95
1.3876-1.40830.30722560.31565263X-RAY DIFFRACTION97
1.4083-1.43030.29862670.30495288X-RAY DIFFRACTION98
1.4303-1.45380.35132540.28645345X-RAY DIFFRACTION97
1.4538-1.47890.28763030.2795274X-RAY DIFFRACTION97
1.4789-1.50580.29942810.26715339X-RAY DIFFRACTION98
1.5058-1.53470.26832790.25245302X-RAY DIFFRACTION98
1.5347-1.5660.28142990.24195350X-RAY DIFFRACTION98
1.566-1.60010.25813000.23955354X-RAY DIFFRACTION98
1.6001-1.63730.28982950.23585359X-RAY DIFFRACTION98
1.6373-1.67830.22662930.23015212X-RAY DIFFRACTION97
1.6783-1.72370.25762750.22125388X-RAY DIFFRACTION98
1.7237-1.77440.24432920.21185362X-RAY DIFFRACTION98
1.7744-1.83170.23712630.21595440X-RAY DIFFRACTION99
1.8317-1.89710.21722910.20425422X-RAY DIFFRACTION99
1.8971-1.97310.21592730.19255450X-RAY DIFFRACTION99
1.9731-2.06290.21462700.19225452X-RAY DIFFRACTION99
2.0629-2.17160.20842630.18675513X-RAY DIFFRACTION99
2.1716-2.30770.19772890.18765390X-RAY DIFFRACTION98
2.3077-2.48590.2143220.18645442X-RAY DIFFRACTION99
2.4859-2.73610.223250.18975485X-RAY DIFFRACTION99
2.7361-3.1320.2173190.19525540X-RAY DIFFRACTION100
3.132-3.94580.17552980.17335590X-RAY DIFFRACTION100

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