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- PDB-8a8z: Crystal structure of Danio rerio HDAC6 CD2 in complex with in sit... -

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Basic information

Entry
Database: PDB / ID: 8a8z
TitleCrystal structure of Danio rerio HDAC6 CD2 in complex with in situ enzymatically hydrolyzed DFMO-based ITF5924
ComponentsHistone deacetylase 6HDAC6
KeywordsHYDROLASE / HISTONE DEACETYLASE / COMPLEX WITH HYDRAZIDE / NON-HYDROXAMATE ZINC BINDING GROUP / MECHANISM-BASED INHIBITOR
Function / homology
Function and homology information


: / Aggrephagy / : / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / histone deacetylase activity / regulation of tubulin deacetylation / potassium ion binding ...: / Aggrephagy / : / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / histone deacetylase activity / regulation of tubulin deacetylation / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation / angiogenesis / negative regulation of transcription by RNA polymerase II / 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
: / Chem-LDL / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZrubek, K. / Sandrone, G. / Cukier, C.D. / Stevenazzi, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Regional Development FundE79J19000480007 - ID 1165235European Union
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Difluoromethyl-1,3,4-oxadiazoles are slow-binding substrate analog inhibitors of histone deacetylase 6 with unprecedented isotype selectivity.
Authors: Cellupica, E. / Caprini, G. / Cordella, P. / Cukier, C. / Fossati, G. / Marchini, M. / Rocchio, I. / Sandrone, G. / Vanoni, M.A. / Vergani, B. / Zrubek, K. / Stevenazzi, A. / Steinkuhler, C.
History
DepositionJun 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)81,72510
Polymers80,6852
Non-polymers1,0408
Water12,358686
1
A: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8635
Polymers40,3431
Non-polymers5204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8635
Polymers40,3431
Non-polymers5204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.372, 118.924, 60.263
Angle α, β, γ (deg.)90.000, 93.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histone deacetylase 6 / HDAC6


Mass: 40342.535 Da / Num. of mol.: 2
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-LDL / 4-[[4-[4-(imidazolidin-2-ylideneamino)phenyl]-1,2,3-triazol-1-yl]methyl]benzohydrazide


Mass: 376.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20N8O / 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.: 4 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 686 / 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: 2.36 Å3/Da / Density % sol: 47.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Na-citrate pH 6.5, 20% (v/v) PEG4000, 20% (v/v) isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1.283 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 1.6→47.88 Å / Num. obs: 92341 / % possible obs: 95.6 % / Redundancy: 7.5 % / Biso Wilson estimate: 19.05 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.052 / Rrim(I) all: 0.143 / Net I/σ(I): 8.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 7.4 % / Rmerge(I) obs: 2.494 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4419 / CC1/2: 0.37 / Rpim(I) all: 1.356 / Rsym value: 2.683 / % possible all: 91.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSVERSION Mar 15, 2019 BUILT=20191015data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EEK

5eek


Resolution: 1.6→47.88 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.292 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1903 4695 5.1 %RANDOM
Rwork0.155 ---
obs0.1568 87601 95.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.38 Å2 / Biso mean: 23.673 Å2 / Biso min: 13.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0 Å2-0.81 Å2
2--1.03 Å20 Å2
3----0.72 Å2
Refinement stepCycle: final / Resolution: 1.6→47.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5580 0 62 686 6328
Biso mean--35.34 36.49 -
Num. residues----714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135845
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175331
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.6357950
X-RAY DIFFRACTIONr_angle_other_deg1.4791.5712286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4085736
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95320.943318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91215932
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3611544
X-RAY DIFFRACTIONr_chiral_restr0.0830.2750
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026742
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021394
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 347 -
Rwork0.315 6242 -
all-6589 -
obs--92.03 %

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