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- PDB-5wgi: Ultrahigh resolution crystal structure of Danio rerio histone dea... -

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Basic information

Entry
Database: PDB / ID: 5wgi
TitleUltrahigh resolution crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with TSA
ComponentsHdac6 protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / histone deacetylase / hydrolase inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of cellular component organization / positive regulation of cellular component organization / Aggrephagy / regulation of biological quality / deacetylase activity / tubulin deacetylase activity / mitochondrion localization / swimming behavior / definitive hemopoiesis / regulation of microtubule-based process ...negative regulation of cellular component organization / positive regulation of cellular component organization / Aggrephagy / regulation of biological quality / deacetylase activity / tubulin deacetylase activity / mitochondrion localization / swimming behavior / definitive hemopoiesis / regulation of microtubule-based process / protein lysine deacetylase activity / histone deacetylase activity / response to stress / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation / epigenetic regulation of gene expression / transferase activity / actin binding / chromatin organization / angiogenesis / perikaryon / axon / dendrite / centrosome / zinc ion binding / nucleus / cytoplasm / cytosol
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
: / DI(HYDROXYETHYL)ETHER / TRICHOSTATIN A / Protein deacetylase HDAC6 / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsPorter, N.J. / Christianson, D.W.
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 1.3Oct 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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)41,90923
Polymers40,2851
Non-polymers1,62422
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-52 kcal/mol
Surface area13690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.439, 69.639, 50.193
Angle α, β, γ (deg.)90.00, 110.42, 90.00
Int Tables number4
Space group name H-MP1211

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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 , 9 types, 446 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TSN / TRICHOSTATIN A / 7-[4-(DIMETHYLAMINO)PHENYL]-N-HYDROXY-4,6-DIMETHYL-7-OXO-2,4-HEPTADIENAMIDE


Mass: 302.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H22N2O3
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 1.97 Å3/Da / Density % sol: 37.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: magnesium chloride, Bis-Tris, pH 6.5, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 7, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.05→47.04 Å / Num. obs: 138710 / % possible obs: 95.6 % / Redundancy: 3.3 % / Net I/σ(I): 11.1
Reflection shellHighest resolution: 1.05 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_2776: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5EEM

5eem


Resolution: 1.05→47.038 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 11.34
RfactorNum. reflection% reflection
Rfree0.1255 6928 5 %
Rwork0.1063 --
obs0.1072 138677 95.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.05→47.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2787 0 97 424 3308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093185
X-RAY DIFFRACTIONf_angle_d1.1484312
X-RAY DIFFRACTIONf_dihedral_angle_d23.0111178
X-RAY DIFFRACTIONf_chiral_restr0.087450
X-RAY DIFFRACTIONf_plane_restr0.009577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.06190.24272270.24534097X-RAY DIFFRACTION90
1.0619-1.07440.25492220.22384136X-RAY DIFFRACTION90
1.0744-1.08750.22382170.20984157X-RAY DIFFRACTION91
1.0875-1.10130.19331930.19284223X-RAY DIFFRACTION91
1.1013-1.11580.19272160.18124203X-RAY DIFFRACTION92
1.1158-1.13110.19682240.16734284X-RAY DIFFRACTION93
1.1311-1.14720.16172080.16424319X-RAY DIFFRACTION94
1.1472-1.16440.18242400.14654286X-RAY DIFFRACTION94
1.1644-1.18260.17672170.14364353X-RAY DIFFRACTION95
1.1826-1.2020.15452320.13654388X-RAY DIFFRACTION95
1.202-1.22270.16482450.12684386X-RAY DIFFRACTION96
1.2227-1.24490.13992400.11574395X-RAY DIFFRACTION96
1.2449-1.26890.15412230.10854407X-RAY DIFFRACTION96
1.2689-1.29480.13072150.11234446X-RAY DIFFRACTION97
1.2948-1.32290.13162440.09944446X-RAY DIFFRACTION97
1.3229-1.35370.12292400.08894459X-RAY DIFFRACTION97
1.3537-1.38760.1182340.08614475X-RAY DIFFRACTION97
1.3876-1.42510.11952530.0874466X-RAY DIFFRACTION98
1.4251-1.4670.10192670.0794472X-RAY DIFFRACTION98
1.467-1.51440.10372400.07614486X-RAY DIFFRACTION98
1.5144-1.56850.1142340.07564478X-RAY DIFFRACTION97
1.5685-1.63130.1072410.0764480X-RAY DIFFRACTION98
1.6313-1.70550.11032270.07654541X-RAY DIFFRACTION98
1.7055-1.79550.09872500.07714532X-RAY DIFFRACTION98
1.7955-1.9080.11092470.07944442X-RAY DIFFRACTION98
1.908-2.05530.0992400.08264477X-RAY DIFFRACTION97
2.0553-2.26210.10672340.08224458X-RAY DIFFRACTION96
2.2621-2.58940.11012090.09344485X-RAY DIFFRACTION97
2.5894-3.26230.10462390.10554465X-RAY DIFFRACTION96
3.2623-47.08520.12562100.12534507X-RAY DIFFRACTION95

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