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- PDB-8g20: Crystal Structure of Danio rerio histone deacetylase 6 catalytic ... -

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Basic information

Entry
Database: PDB / ID: 8g20
TitleCrystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with inhibitor Mz327
ComponentsHdac6 protein
KeywordsHYDROLASE/INHIBITOR / histone deacetylase / inhibitor / metallohydrolase / hydrolase-inhibitor complex / HYDROLASE
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
ETHANOL / : / 4-[(N-butylpentanamido)methyl]-N-hydroxybenzamide / Hdac6 protein
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.766 Å
AuthorsTararina, M.A. / 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: J.Med.Chem. / Year: 2023
Title: Development of First-in-Class Dual Sirt2/HDAC6 Inhibitors as Molecular Tools for Dual Inhibition of Tubulin Deacetylation.
Authors: Sinatra, L. / Vogelmann, A. / Friedrich, F. / Tararina, M.A. / Neuwirt, E. / Colcerasa, A. / Konig, P. / Toy, L. / Yesiloglu, T.Z. / Hilscher, S. / Gaitzsch, L. / Papenkordt, N. / Zhai, S. / ...Authors: Sinatra, L. / Vogelmann, A. / Friedrich, F. / Tararina, M.A. / Neuwirt, E. / Colcerasa, A. / Konig, P. / Toy, L. / Yesiloglu, T.Z. / Hilscher, S. / Gaitzsch, L. / Papenkordt, N. / Zhai, S. / Zhang, L. / Romier, C. / Einsle, O. / Sippl, W. / Schutkowski, M. / Gross, O. / Bendas, G. / Christianson, D.W. / Hansen, F.K. / Jung, M. / Schiedel, M.
History
DepositionFeb 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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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)81,98219
Polymers80,5712
Non-polymers1,41117
Water7,206400
1
A: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9689
Polymers40,2851
Non-polymers6828
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,01410
Polymers40,2851
Non-polymers7289
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.244, 55.544, 74.399
Angle α, β, γ (deg.)73.00, 89.90, 82.82
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hdac6 protein / Histone Deacetylase 6


Mass: 40285.484 Da / Num. of mol.: 2 / Fragment: catalytic domain 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7YT55

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Non-polymers , 6 types, 417 molecules

#2: Chemical ChemComp-YJ5 / 4-[(N-butylpentanamido)methyl]-N-hydroxybenzamide


Mass: 306.400 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C17H26N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.38 Å3/Da / Density % sol: 48.34 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop
Details: 0.1 M bis-Tris (pH 6.0), 0.2 M KSCN, 20% PEG 3350 (w/v), 3% (v/v) ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.766→29.05 Å / Num. obs: 69137 / % possible obs: 96.1 % / Redundancy: 2.7 % / Biso Wilson estimate: 13.91 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.131 / Rsym value: 0.121 / Net I/σ(I): 5.4
Reflection shellResolution: 1.776→1.81 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 6517 / CC1/2: 0.649 / Rpim(I) all: 0.352 / % possible all: 89.2

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.766→29.047 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2305 2000 2.89 %
Rwork0.1932 --
obs0.1942 69115 96.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.766→29.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5489 0 83 400 5972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015716
X-RAY DIFFRACTIONf_angle_d1.0287750
X-RAY DIFFRACTIONf_dihedral_angle_d10.4754602
X-RAY DIFFRACTIONf_chiral_restr0.063846
X-RAY DIFFRACTIONf_plane_restr0.0071013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7662-1.81030.37241340.29074495X-RAY DIFFRACTION90
1.8103-1.85930.28051420.25924773X-RAY DIFFRACTION96
1.8593-1.9140.27911430.234793X-RAY DIFFRACTION96
1.914-1.97570.24591410.21524745X-RAY DIFFRACTION96
1.9757-2.04630.25181430.2094778X-RAY DIFFRACTION96
2.0463-2.12820.24761430.20234812X-RAY DIFFRACTION96
2.1282-2.22510.23471440.19834837X-RAY DIFFRACTION97
2.2251-2.34230.25351440.19054813X-RAY DIFFRACTION97
2.3423-2.4890.22431430.19174813X-RAY DIFFRACTION97
2.489-2.68110.22141450.19174860X-RAY DIFFRACTION97
2.6811-2.95060.23521440.1954833X-RAY DIFFRACTION97
2.9506-3.3770.22691440.19524852X-RAY DIFFRACTION97
3.377-4.25260.20011450.16584858X-RAY DIFFRACTION97
4.2526-29.0470.18021450.15784853X-RAY DIFFRACTION97

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