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

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Basic information

Entry
Database: PDB / ID: 9ggk
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (CD2) in complex with N-((6-(Hydroxyamino)-6-oxohexyl)oxy)-4-(4-methoxyphenyl)thiazole-2-carboxamide
ComponentsHistone deacetylase 6
KeywordsHYDROLASE / Histone deacetylase / zinc enzyme / inhibitor
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
: / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHebeis, M. / Fischer, F. / Kurz, T. / Span, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
Not funded Germany
CitationJournal: J.Med.Chem. / Year: 2024
Title: Deciphering the Therapeutic Potential of Novel Pentyloxyamide-Based Class I, IIb HDAC Inhibitors against Therapy-Resistant Leukemia.
Authors: Fischer, F. / Schliehe-Diecks, J. / Tu, J.W. / Gangnus, T. / Ho, Y.L. / Hebeis, M. / Alves Avelar, L.A. / Scharov, K. / Watrin, T. / Kemkes, M. / Stachura, P. / Daugs, K. / Biermann, L. / ...Authors: Fischer, F. / Schliehe-Diecks, J. / Tu, J.W. / Gangnus, T. / Ho, Y.L. / Hebeis, M. / Alves Avelar, L.A. / Scharov, K. / Watrin, T. / Kemkes, M. / Stachura, P. / Daugs, K. / Biermann, L. / Kremeyer, J. / Horstick, N. / Span, I. / Pandyra, A.A. / Borkhardt, A. / Gohlke, H. / Kassack, M.U. / Burckhardt, B.B. / Bhatia, S. / Kurz, T.
History
DepositionAug 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: 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

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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)40,9276
Polymers40,2851
Non-polymers6415
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-119 kcal/mol
Surface area13060 Å2
Unit cell
Length a, b, c (Å)42.278, 87.098, 179.771
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-975-

HOH

21A-978-

HOH

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Components

#1: Protein Histone deacetylase 6


Mass: 40285.484 Da / Num. of mol.: 1
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-A1IK2 / 4-(4-methoxyphenyl)-~{N}-[6-(oxidanylamino)-6-oxidanylidene-hexoxy]-1,3-thiazole-2-carboxamide


Mass: 379.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N3O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.05 Å3/Da / Density % sol: 40.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate, 0.1 sodium formate, 28% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jan 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.9→44.983 Å / Num. obs: 25240 / % possible obs: 94.6 % / Redundancy: 7.5 % / CC1/2: 0.995 / Net I/σ(I): 9.4
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 6.8 % / Num. unique obs: 1550 / CC1/2: 0.453 / % possible all: 90.6

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Processing

Software
NameVersionClassification
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
REFMAC5.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→44.983 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.911 / SU B: 5.411 / SU ML: 0.144 / Cross valid method: FREE R-VALUE / ESU R: 0.199 / ESU R Free: 0.183 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2672 1260 5.002 %
Rwork0.208 23929 -
all0.211 --
obs-25189 94.172 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.196 Å20 Å20 Å2
2---0.852 Å2-0 Å2
3---0.656 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 0 30 80 2854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122892
X-RAY DIFFRACTIONr_angle_refined_deg1.8761.823930
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7155364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.9457.58629
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20410462
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.39410136
X-RAY DIFFRACTIONr_chiral_restr0.1140.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022250
X-RAY DIFFRACTIONr_nbd_refined0.2150.21389
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21962
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2141
X-RAY DIFFRACTIONr_metal_ion_refined0.0430.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2140.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1680.29
X-RAY DIFFRACTIONr_mcbond_it2.152.5161429
X-RAY DIFFRACTIONr_mcangle_it3.0924.5061790
X-RAY DIFFRACTIONr_scbond_it3.2022.841463
X-RAY DIFFRACTIONr_scangle_it4.8185.052136
X-RAY DIFFRACTIONr_lrange_it6.12529.6724460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.612740.6121690X-RAY DIFFRACTION90.4615
1.949-2.0030.664970.5831685X-RAY DIFFRACTION93.2008
2.003-2.060.463980.4581578X-RAY DIFFRACTION92.24
2.06-2.1240.348960.321571X-RAY DIFFRACTION91.1926
2.124-2.1930.311800.2481531X-RAY DIFFRACTION92.5862
2.193-2.270.287670.2131497X-RAY DIFFRACTION94.0469
2.27-2.3550.282820.1921429X-RAY DIFFRACTION92.9846
2.355-2.4510.233690.1911394X-RAY DIFFRACTION93.4227
2.451-2.560.273630.1961368X-RAY DIFFRACTION94.021
2.56-2.6850.234620.1961300X-RAY DIFFRACTION94.5833
2.685-2.8290.284680.1941262X-RAY DIFFRACTION95.8213
2.829-30.234640.1891184X-RAY DIFFRACTION96.0739
3-3.2060.217570.1841153X-RAY DIFFRACTION97.4235
3.206-3.4620.226590.182928X-RAY DIFFRACTION86.2762
3.462-3.790.231540.162993X-RAY DIFFRACTION98.4948
3.79-4.2330.223460.156928X-RAY DIFFRACTION100
4.233-4.8810.142370.138826X-RAY DIFFRACTION99.7688
4.881-5.9610.236350.193708X-RAY DIFFRACTION100
5.961-8.3560.305310.213560X-RAY DIFFRACTION100
8.356-44.9830.309210.198344X-RAY DIFFRACTION99.455

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