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- PDB-8bjk: X-ray structure of Danio rerio histone deacetylase 6 (HDAC6) CD2 ... -

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Basic information

Entry
Database: PDB / ID: 8bjk
TitleX-ray structure of Danio rerio histone deacetylase 6 (HDAC6) CD2 in complex with an inhibitor CPD11352
ComponentsHistone deacetylase 6
KeywordsHYDROLASE / HISTONE DEACETYLASE / DEACETYLATION / INHIBITOR / DANIO RERIO
Function / homology
Function and homology information


Aggrephagy / negative regulation of cellular component organization / positive regulation of cellular component organization / regulation of biological quality / deacetylase activity / tubulin deacetylase activity / mitochondrion localization / swimming behavior / definitive hemopoiesis / regulation of microtubule-based process ...Aggrephagy / negative regulation of cellular component organization / positive regulation of cellular component organization / regulation of biological quality / deacetylase activity / tubulin deacetylase activity / mitochondrion localization / swimming behavior / definitive hemopoiesis / regulation of microtubule-based process / protein lysine deacetylase activity / potassium ion binding / response to stress / hematopoietic progenitor cell differentiation / transferase activity / actin binding / chromatin organization / angiogenesis / perikaryon / axon / dendrite / centrosome / zinc ion binding / nucleus / cytoplasm / cytosol
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
: / Chem-QXF / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.35 Å
AuthorsBarinka, C. / Motlova, L. / Pavlicek, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Chem.Biol. / Year: 2023
Title: Comprehensive Mechanistic View of the Hydrolysis of Oxadiazole-Based Inhibitors by Histone Deacetylase 6 (HDAC6).
Authors: Motlova, L. / Snajdr, I. / Kutil, Z. / Andris, E. / Ptacek, J. / Novotna, A. / Novakova, Z. / Havlinova, B. / Tueckmantel, W. / Draberova, H. / Majer, P. / Schutkowski, M. / Kozikowski, A. / ...Authors: Motlova, L. / Snajdr, I. / Kutil, Z. / Andris, E. / Ptacek, J. / Novotna, A. / Novakova, Z. / Havlinova, B. / Tueckmantel, W. / Draberova, H. / Majer, P. / Schutkowski, M. / Kozikowski, A. / Rulisek, L. / Barinka, C.
History
DepositionNov 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release

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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)40,3985
Polymers39,8991
Non-polymers4984
Water6,648369
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-0 kcal/mol
Surface area13080 Å2
Unit cell
Length a, b, c (Å)51.490, 83.780, 94.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Histone deacetylase 6


Mass: 39899.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Cell line (production host): HEK293T / Organ (production host): kidney / Production host: Homo sapiens (human) / References: UniProt: F8W4B7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-QXF / ~{N}-[[5-(aminocarbamoyl)pyridin-2-yl]methyl]-~{N}-(3-chlorophenyl)methanesulfonamide


Mass: 354.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15ClN4O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 19% PEG 3350 (SIGMA-ALDRICH), 0.2 M KSCN (HAMPTON RESEARCH), 0.1 M BIS-TRIS Ph 6.5 (SIGMA-ALDRICH)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Mar 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 1.35→62.64 Å / Num. obs: 90048 / % possible obs: 99.9 % / Redundancy: 15 % / CC1/2: 0.999 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.032 / Rrim(I) all: 0.125 / Net I/σ(I): 17.9
Reflection shellResolution: 1.35→1.37 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4356 / CC1/2: 0.3 / Rpim(I) all: 0.923 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6r0k

6r0k


Resolution: 1.35→62.64 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.446 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2073 4531 5 %RANDOM
Rwork0.16807 ---
obs0.17002 85454 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.072 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å2-0 Å2
2---0.34 Å20 Å2
3---0.4 Å2
Refinement stepCycle: 1 / Resolution: 1.35→62.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2751 0 26 369 3146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192938
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.9394003
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5775376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41123.259135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74215472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1781521
X-RAY DIFFRACTIONr_chiral_restr0.0960.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212287
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.2331.2231459
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4721.8291835
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9141.4231479
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined2.80811.4394898
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.46232938
X-RAY DIFFRACTIONr_sphericity_free30.0915129
X-RAY DIFFRACTIONr_sphericity_bonded9.42153102
LS refinement shellResolution: 1.351→1.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 327 -
Rwork0.333 6218 -
obs--99.09 %

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