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- PDB-7o2r: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -

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Basic information

Entry
Database: PDB / ID: 7o2r
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with ITF3985
ComponentsHistone deacetylase 6
KeywordsHYDROLASE / histone deacetylase / complex with hydroxamate inhibitor
Function / homology
Function and homology information


Aggrephagy / 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 ...Aggrephagy / 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
IODIDE ION / : / DI(HYDROXYETHYL)ETHER / Chem-V05 / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsZrubek, K. / Sandrone, G. / Cukier, C.D. / Stevenazzi, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
European Regional Development FundProject E79J19000480007 - ID 1165235 Italy
CitationJournal: Acs Med.Chem.Lett. / Year: 2021
Title: Role of Fluorination in the Histone Deacetylase 6 (HDAC6) Selectivity of Benzohydroxamate-Based Inhibitors.
Authors: Sandrone, G. / Cukier, C.D. / Zrubek, K. / Marchini, M. / Vergani, B. / Caprini, G. / Fossati, G. / Steinkuhler, C. / Stevenazzi, A.
History
DepositionMar 31, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,68712
Polymers40,3431
Non-polymers1,34411
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-1 kcal/mol
Surface area13570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.966, 84.212, 94.977
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Histone deacetylase 6


Mass: 40342.535 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

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Non-polymers , 6 types, 108 molecules

#2: Chemical ChemComp-V05 / 3,5-bis(fluoranyl)-~{N}-oxidanyl-4-[(5-pyrimidin-2-yl-1,2,3,4-tetrazol-2-yl)methyl]benzamide


Mass: 333.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H9F2N7O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.58 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Bis-Tris propane pH 8.5, 0.2 M sodium iodide, 19% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→47.49 Å / Num. obs: 17684 / % possible obs: 91.8 % / Redundancy: 13 % / CC1/2: 0.996 / Rmerge(I) obs: 0.255 / Rpim(I) all: 0.072 / Rrim(I) all: 0.266 / Net I/σ(I): 9.6 / Num. measured all: 230764
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.389.61.5771720818000.690.5241.6661.697.4
8.9-47.4910.40.05341263950.9990.0170.05632.599.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSVERSION Mar 15, 2019 BUILT=20191015data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5eek

5eek


Resolution: 2.3→45.63 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.904 / SU B: 9.369 / SU ML: 0.214 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.366 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2599 895 5.1 %RANDOM
Rwork0.1993 ---
obs0.2025 16740 91.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 147.22 Å2 / Biso mean: 33.176 Å2 / Biso min: 3.89 Å2
Baniso -1Baniso -2Baniso -3
1-3.93 Å20 Å2-0 Å2
2---3.91 Å20 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 2.3→45.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2790 0 40 97 2927
Biso mean--54.83 31.03 -
Num. residues----357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132893
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172594
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.6343923
X-RAY DIFFRACTIONr_angle_other_deg1.3171.5666007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4045356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74521.083157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19515460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5641522
X-RAY DIFFRACTIONr_chiral_restr0.0750.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023278
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02635
LS refinement shellResolution: 2.3→2.357 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.354 67 -
Rwork0.313 1284 -
obs--96.43 %

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