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- PDB-7o2p: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -

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Basic information

Entry
Database: PDB / ID: 7o2p
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with ITF3756
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 / 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
IODIDE ION / : / DI(HYDROXYETHYL)ETHER / Chem-UZW / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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
B: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,43627
Polymers80,6852
Non-polymers2,75125
Water3,837213
1
A: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,58313
Polymers40,3431
Non-polymers1,24012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,85314
Polymers40,3431
Non-polymers1,51113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.483, 90.753, 71.964
Angle α, β, γ (deg.)90.000, 95.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Histone deacetylase 6


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

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Non-polymers , 9 types, 238 molecules

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


Mass: 301.324 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11N5O2S / 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 1.95 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Bis-Tris propane pH 7.5, 0.2 M sodium nitrate, 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.9→48.25 Å / Num. obs: 48867 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 23.3 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.072 / Rrim(I) all: 0.191 / Χ2: 1 / Net I/σ(I): 7.2
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.977 / Mean I/σ(I) obs: 1 / Num. unique obs: 3154 / CC1/2: 0.608 / Rpim(I) all: 0.803 / Rrim(I) all: 2.136 / Χ2: 1 / % possible all: 100

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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: 1.9→45.42 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.869 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 2406 4.9 %RANDOM
Rwork0.1946 ---
obs0.1978 46434 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 126.15 Å2 / Biso mean: 32.075 Å2 / Biso min: 16.49 Å2
Baniso -1Baniso -2Baniso -3
1-2.98 Å20 Å2-2.59 Å2
2---0.11 Å20 Å2
3----2.31 Å2
Refinement stepCycle: final / Resolution: 1.9→45.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5573 0 139 213 5925
Biso mean--36.34 33.72 -
Num. residues----713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135834
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175265
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.6367887
X-RAY DIFFRACTIONr_angle_other_deg1.31.56712189
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3935711
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.66221.083314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.41815920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6511544
X-RAY DIFFRACTIONr_chiral_restr0.0750.2737
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026557
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021273
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 175 -
Rwork0.356 3427 -
all-3602 -
obs--99.94 %

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