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

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Basic information

Entry
Database: PDB / ID: 7jom
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with TO-317
ComponentsHdac6 protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Hydrolase / histone deacetylase / inhibitor / metallohydrolase / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


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 ...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
FORMIC ACID / : / Chem-TO3 / Hdac6 protein
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsWatson, P.R. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM49758 United States
CitationJournal: J.Med.Chem. / Year: 2021
Title: Unique Molecular Interaction with the Histone Deacetylase 6 Catalytic Tunnel: Crystallographic and Biological Characterization of a Model Chemotype.
Authors: Olaoye, O.O. / Watson, P.R. / Nawar, N. / Geletu, M. / Sedighi, A. / Bukhari, S. / Raouf, Y.S. / Manaswiyoungkul, P. / Erdogan, F. / Abdeldayem, A. / Cabral, A.D. / Hassan, M.M. / Toutah, K. ...Authors: Olaoye, O.O. / Watson, P.R. / Nawar, N. / Geletu, M. / Sedighi, A. / Bukhari, S. / Raouf, Y.S. / Manaswiyoungkul, P. / Erdogan, F. / Abdeldayem, A. / Cabral, A.D. / Hassan, M.M. / Toutah, K. / Shouksmith, A.E. / Gawel, J.M. / Israelian, J. / Radu, T.B. / Kachhiyapatel, N. / de Araujo, E.D. / Christianson, D.W. / Gunning, P.T.
History
DepositionAug 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Hdac6 protein
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,20618
Polymers80,5712
Non-polymers1,63516
Water6,864381
1
A: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,20011
Polymers40,2851
Non-polymers91410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0077
Polymers40,2851
Non-polymers7216
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.460, 96.450, 96.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hdac6 protein / Histone Deacetylase 6


Mass: 40285.484 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: A7YT55, Hydrolases

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Non-polymers , 6 types, 397 molecules

#2: Chemical ChemComp-TO3 / N-hydroxy-4-({[(pyridin-3-yl)methyl][(2,3,4,5-tetrafluorophenyl)sulfonyl]amino}methyl)benzamide


Mass: 469.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H15F4N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL protein, 0.2 M potassium formate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 12, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.84→68.2 Å / Num. obs: 62134 / % possible obs: 99.3 % / Redundancy: 6.3 % / Biso Wilson estimate: 9.93 Å2 / CC1/2: 0.994 / Net I/σ(I): 9
Reflection shellResolution: 1.84→1.902 Å / Num. unique obs: 11945 / CC1/2: 0.956

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5EEM

5eem


Resolution: 1.84→59.43 Å / SU ML: 0.161 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1803 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2071 3207 5.22 %
Rwork0.1677 58274 -
obs0.1697 61481 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.35 Å2
Refinement stepCycle: LAST / Resolution: 1.84→59.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5466 0 95 381 5942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01075712
X-RAY DIFFRACTIONf_angle_d0.90337756
X-RAY DIFFRACTIONf_chiral_restr0.0528841
X-RAY DIFFRACTIONf_plane_restr0.0071009
X-RAY DIFFRACTIONf_dihedral_angle_d10.64313960
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.860.24521300.18662500X-RAY DIFFRACTION98.24
1.86-1.890.25241210.18722508X-RAY DIFFRACTION97.81
1.89-1.920.22691350.17832469X-RAY DIFFRACTION98.6
1.92-1.960.28261070.17962508X-RAY DIFFRACTION98.64
1.96-1.990.21661330.17562501X-RAY DIFFRACTION98.58
1.99-2.030.2081270.16952498X-RAY DIFFRACTION98.61
2.03-2.070.22111640.15862476X-RAY DIFFRACTION98.69
2.07-2.120.23911590.15732471X-RAY DIFFRACTION98.58
2.12-2.170.19551420.16312501X-RAY DIFFRACTION98.91
2.17-2.220.23581490.16042522X-RAY DIFFRACTION99.04
2.22-2.280.20261040.16322532X-RAY DIFFRACTION98.95
2.28-2.350.20031430.16492527X-RAY DIFFRACTION98.71
2.35-2.420.23181680.15962472X-RAY DIFFRACTION98.91
2.42-2.510.22171520.16452512X-RAY DIFFRACTION99.37
2.51-2.610.17131680.16242525X-RAY DIFFRACTION99.19
2.61-2.730.21171330.1632548X-RAY DIFFRACTION99.52
2.73-2.870.18431570.17032496X-RAY DIFFRACTION99.21
2.87-3.050.19281210.17392583X-RAY DIFFRACTION99.45
3.05-3.290.17751440.18192567X-RAY DIFFRACTION99.49
3.29-3.620.20351330.1642587X-RAY DIFFRACTION99.63
3.62-4.140.18731490.16412582X-RAY DIFFRACTION99.6
4.14-5.220.18121150.15312646X-RAY DIFFRACTION99.42
5.22-59.430.22621530.18082743X-RAY DIFFRACTION98.94

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