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- PDB-8gd4: Crystal Structure of Danio rerio histone deacetylase 6 catalytic ... -

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Basic information

Entry
Database: PDB / ID: 8gd4
TitleCrystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with DMFO Inhibitor 6
ComponentsHdac6 protein
KeywordsHYDROLASE / histone deacetylase / inhibitor / metallohydrolase
Function / homology
Function and homology information


tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / 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
: / Chem-Z4I / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWatson, P.R. / Craigin, A.D. / 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: 2023
Title: Difluoromethyl-1,3,4-oxadiazoles Are Selective, Mechanism-Based, and Essentially Irreversible Inhibitors of Histone Deacetylase 6 .
Authors: Konig, B. / Watson, P.R. / Ressing, N. / Cragin, A.D. / Schaker-Hubner, L. / Christianson, D.W. / Hansen, F.K.
History
DepositionMar 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)81,50110
Polymers80,5712
Non-polymers9308
Water7,638424
1
A: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7505
Polymers40,2851
Non-polymers4654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7505
Polymers40,2851
Non-polymers4654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.803, 92.364, 96.474
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 442 through 496 or (resid 497...
d_2ens_1(chain "B" and (resid 442 through 477 or (resid 478...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROILEA1 - 67
d_12ens_1ILESERA69 - 192
d_13ens_1HISGLYA194 - 218
d_14ens_1GLYALAA220 - 249
d_15ens_1GLUALAA251 - 266
d_16ens_1GLYMETA268 - 313
d_17ens_1METASPA315 - 329
d_18ens_1PROLEUA333 - 356
d_19ens_1LIGLIGB
d_21ens_1PROILEC1 - 67
d_22ens_1ILESERC69 - 192
d_23ens_1HISGLYC194 - 218
d_24ens_1GLYALAC220 - 249
d_25ens_1GLUALAC251 - 266
d_26ens_1GLYMETC268 - 313
d_27ens_1METLEUC315 - 353
d_28ens_1LIGLIGD

NCS oper: (Code: givenMatrix: (-0.999957903051, -0.00536899678441, -0.00744083328878), (-0.0054463696417, 0.999930904444, 0.0104174562916), (0.00738438787093, 0.010457543277, -0.999918051944)Vector: ...NCS oper: (Code: given
Matrix: (-0.999957903051, -0.00536899678441, -0.00744083328878), (-0.0054463696417, 0.999930904444, 0.0104174562916), (0.00738438787093, 0.010457543277, -0.999918051944)
Vector: 74.7669561542, 0.0918326263806, 22.0514345225)

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Components

#1: Protein Hdac6 protein / Histone Deacetylase 6


Mass: 40285.484 Da / Num. of mol.: 2 / Fragment: catalytic domain 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
#2: Chemical ChemComp-Z4I / 2-(benzylamino)-N'-(difluoroacetyl)pyrimidine-5-carbohydrazide


Mass: 321.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H13F2N5O2 / 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


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.07 Å3/Da / Density % sol: 40.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL HDAC6 Protein, 0.04 M citric acid, 0.06 M bis-Tris propane (pH 5.0), 16% (w/v) polyethylene glycol 3,350

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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: 0.9793 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→36.216 Å / Num. obs: 90179 / % possible obs: 99.5 % / Redundancy: 1.9 % / Biso Wilson estimate: 15.44 Å2 / CC1/2: 0.993 / Net I/σ(I): 7.3
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 8857 / CC1/2: 0.851

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Processing

Software
NameVersionClassification
XDS1.20.1_4487data reduction
PHENIX1.20.1_4487refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.56 Å / SU ML: 0.2131 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.0642
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2223 2003 4.37 %
Rwork0.185 43805 -
obs0.1867 45808 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.82 Å2
Refinement stepCycle: LAST / Resolution: 2→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5423 0 52 424 5899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00755663
X-RAY DIFFRACTIONf_angle_d0.95637702
X-RAY DIFFRACTIONf_chiral_restr0.0564846
X-RAY DIFFRACTIONf_plane_restr0.01171003
X-RAY DIFFRACTIONf_dihedral_angle_d25.476791
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.499877909733 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.26371330.23192932X-RAY DIFFRACTION93.99
2.05-2.10.25121440.21853087X-RAY DIFFRACTION99.97
2.1-2.160.30331380.20383068X-RAY DIFFRACTION100
2.16-2.230.23121480.19833112X-RAY DIFFRACTION100
2.23-2.310.23311450.1993134X-RAY DIFFRACTION99.97
2.31-2.410.24211470.18483106X-RAY DIFFRACTION100
2.41-2.520.22931370.19243121X-RAY DIFFRACTION99.94
2.52-2.650.22491420.19153111X-RAY DIFFRACTION99.94
2.65-2.810.2561450.20323126X-RAY DIFFRACTION99.88
2.81-3.030.22591410.19273141X-RAY DIFFRACTION99.85
3.03-3.340.21991480.19853158X-RAY DIFFRACTION99.94
3.34-3.820.2391370.16333188X-RAY DIFFRACTION99.82
3.82-4.810.15291440.14733192X-RAY DIFFRACTION99.94
4.81-29.560.17791540.16873329X-RAY DIFFRACTION99.34

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