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- PDB-8qa7: Crystal structure of HDAC6 catalytic domain 2 from zebrafish in c... -

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Basic information

Entry
Database: PDB / ID: 8qa7
TitleCrystal structure of HDAC6 catalytic domain 2 from zebrafish in complex with buffer component.
ComponentsHistone deacetylase 6
KeywordsMETAL BINDING PROTEIN / HDAC6 / histone deacetylase 6
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: 1.47 Å
AuthorsSandmark, J. / Ek, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2023
Title: Selective and Bioavailable HDAC6 2-(Difluoromethyl)-1,3,4-oxadiazole Substrate Inhibitors and Modeling of Their Bioactivation Mechanism.
Authors: Ripa, L. / Sandmark, J. / Hughes, G. / Shamovsky, I. / Gunnarsson, A. / Johansson, J. / Llinas, A. / Collins, M. / Jung, B. / Noven, A. / Pemberton, N. / Mogemark, M. / Xiong, Y. / Li, Q. / ...Authors: Ripa, L. / Sandmark, J. / Hughes, G. / Shamovsky, I. / Gunnarsson, A. / Johansson, J. / Llinas, A. / Collins, M. / Jung, B. / Noven, A. / Pemberton, N. / Mogemark, M. / Xiong, Y. / Li, Q. / Tangefjord, S. / Ek, M. / Astrand, A.
History
DepositionAug 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone deacetylase 6
B: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,35610
Polymers79,5922
Non-polymers7648
Water4,107228
1
A: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1785
Polymers39,7961
Non-polymers3824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1785
Polymers39,7961
Non-polymers3824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.390, 92.373, 96.190
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 Histone deacetylase 6


Mass: 39796.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Histone deacetylase 6 (HDAC6) catalytic domain 2 from zebrafish. Two molecules in the asymmetric unit.
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Production host: Escherichia coli (E. coli) / References: UniProt: F8W4B7
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M NH4Cl, 20% PEG3350, 2 mM NaAc 10 mg/ml protein mixed 1:1 with well solution Cryo 20% glycerol + well solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 1.47→66.63 Å / Num. obs: 113964 / % possible obs: 99.2 % / Redundancy: 6.1 % / CC1/2: 0.999 / Net I/σ(I): 10.6
Reflection shellResolution: 1.51→1.59 Å / Num. unique obs: 15735 / CC1/2: 0.558

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→66.63 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.527 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23953 5628 4.9 %RANDOM
Rwork0.2171 ---
obs0.21824 108176 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.454 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2--2.04 Å2-0 Å2
3----1.91 Å2
Refinement stepCycle: 1 / Resolution: 1.47→66.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5579 0 36 228 5843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195799
X-RAY DIFFRACTIONr_bond_other_d0.0020.025222
X-RAY DIFFRACTIONr_angle_refined_deg1.311.9447883
X-RAY DIFFRACTIONr_angle_other_deg0.96312117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8555731
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91923.022268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35315926
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9221543
X-RAY DIFFRACTIONr_chiral_restr0.0760.2864
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216506
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021225
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2452.5672876
X-RAY DIFFRACTIONr_mcbond_other1.2422.5662875
X-RAY DIFFRACTIONr_mcangle_it1.9493.8443596
X-RAY DIFFRACTIONr_mcangle_other1.9493.8453597
X-RAY DIFFRACTIONr_scbond_it1.6232.8032923
X-RAY DIFFRACTIONr_scbond_other1.6232.8032923
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5784.1324279
X-RAY DIFFRACTIONr_long_range_B_refined3.76130.6386375
X-RAY DIFFRACTIONr_long_range_B_other3.7630.646376
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.47→1.507 Å
RfactorNum. reflection% reflection
Rfree0.474 400 -
Rwork0.457 7242 -
obs--90.72 %

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