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- PDB-5wgk: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -

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Basic information

Entry
Database: PDB / ID: 5wgk
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with HPB
ComponentsHdac6 protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / histone deacetylase / hydrolase inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
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 domain / Arginase; Chain A / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily ...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 domain / Arginase; Chain A / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Zinc finger, RING/FYVE/PHD-type / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AGJ / IODIDE ION / : / DI(HYDROXYETHYL)ETHER / Hdac6 protein / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.822 Å
AuthorsPorter, N.J. / 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: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Unusual zinc-binding mode of HDAC6-selective hydroxamate inhibitors.
Authors: Porter, N.J. / Mahendran, A. / Breslow, R. / Christianson, D.W.
History
DepositionJul 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,16832
Polymers40,2851
Non-polymers2,88231
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation, monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint34 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.670, 83.970, 94.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-801-

IOD

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hdac6 protein / histone deacetylase 6


Mass: 40285.484 Da / Num. of mol.: 1 / Fragment: catalytic domain 2 (UNP residues 288-646)
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, UniProt: F8W4B7*PLUS

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Non-polymers , 7 types, 440 molecules

#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-AGJ / N-hydroxy-4-{[(2-hydroxyethyl)(phenylacetyl)amino]methyl}benzamide


Mass: 328.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N2O4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O

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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: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: ammonium iodide, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.82→62.79 Å / Num. obs: 37115 / % possible obs: 99.1 % / Redundancy: 5.6 % / Net I/σ(I): 11.7
Reflection shellHighest resolution: 1.82 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5EEM

5eem


Resolution: 1.822→34.883 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1731 1812 4.89 %
Rwork0.149 --
obs0.1502 37057 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.822→34.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2772 0 102 409 3283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113014
X-RAY DIFFRACTIONf_angle_d0.8554064
X-RAY DIFFRACTIONf_dihedral_angle_d19.0431780
X-RAY DIFFRACTIONf_chiral_restr0.055430
X-RAY DIFFRACTIONf_plane_restr0.006533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.822-1.87130.22831270.18272677X-RAY DIFFRACTION99
1.8713-1.92630.21091330.16952696X-RAY DIFFRACTION99
1.9263-1.98850.19231270.15092684X-RAY DIFFRACTION99
1.9885-2.05960.20661370.15032681X-RAY DIFFRACTION99
2.0596-2.1420.19641440.15252660X-RAY DIFFRACTION99
2.142-2.23950.18591500.14652688X-RAY DIFFRACTION99
2.2395-2.35750.18931180.1472701X-RAY DIFFRACTION99
2.3575-2.50520.1751500.15022660X-RAY DIFFRACTION98
2.5052-2.69860.15261490.14932719X-RAY DIFFRACTION99
2.6986-2.970.16721470.15132719X-RAY DIFFRACTION99
2.97-3.39950.15821410.1532715X-RAY DIFFRACTION98
3.3995-4.28170.14991430.13052791X-RAY DIFFRACTION100
4.2817-34.88930.15951460.14832854X-RAY DIFFRACTION97

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