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- PDB-6thv: X-ray structure of the Danio rerio histone deacetylase 6 (HDAC6; ... -

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Basic information

Entry
Database: PDB / ID: 6thv
TitleX-ray structure of the Danio rerio histone deacetylase 6 (HDAC6; catalytic domain 2) in complex with Tubastatin A
ComponentsHistone deacetylase 6
KeywordsHYDROLASE / histone deacetylase 6 / Tubastatin A
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 domain / Arginase; Chain A / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain ...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-N9W / DI(HYDROXYETHYL)ETHER / THIOCYANATE ION / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.1 Å
AuthorsBarinka, C. / Motlova, L. / Svoboda, M.
CitationJournal: Acs Med.Chem.Lett. / Year: 2020
Title: Structural and in Vivo Characterization of Tubastatin A, a Widely Used Histone Deacetylase 6 Inhibitor.
Authors: Shen, S. / Svoboda, M. / Zhang, G. / Cavasin, M.A. / Motlova, L. / McKinsey, T.A. / Eubanks, J.H. / Barinka, C. / Kozikowski, A.P.
History
DepositionNov 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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 / _struct_conn.ptnr2_symmetry
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,98514
Polymers39,8991
Non-polymers1,08613
Water6,648369
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-4 kcal/mol
Surface area13250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.278, 93.713, 51.574
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-808-

SCN

21A-808-

SCN

31A-808-

SCN

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Histone deacetylase 6


Mass: 39899.125 Da / Num. of mol.: 1
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, 382 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-N9W / 4-[(2-methyl-3,4-dihydro-1~{H}-pyrido[4,3-b]indol-5-yl)methyl]-~{N}-oxidanyl-benzamide


Mass: 335.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21N3O2 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.55 Å3/Da / Density % sol: 51.81 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 5.8 / Details: 0.2 M KSCN, 20 % PEG 3350, 0.1 M Bis-Tris, pH5.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.1→46.9 Å / Num. obs: 166560 / % possible obs: 99.6 % / Redundancy: 12.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Net I/σ(I): 17.45
Reflection shellResolution: 1.1→1.16 Å / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 2.94 / Num. unique obs: 26336 / CC1/2: 0.864

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Aimlessdata scaling
REFMACphasing
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5EEK

5eek


Resolution: 1.1→46.9 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.976 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.027
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1688 2101 1.3 %RANDOM
Rwork0.1599 ---
obs0.1601 164453 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 153.99 Å2 / Biso mean: 12.911 Å2 / Biso min: 6.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å2-0 Å2
2--0.94 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: final / Resolution: 1.1→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 0 74 381 3219
Biso mean--45.5 29.37 -
Num. residues----353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0153130
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172714
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.7674253
X-RAY DIFFRACTIONr_angle_other_deg3.6331.7536392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0275402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.57419.392148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.96115465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3811527
X-RAY DIFFRACTIONr_chiral_restr0.1140.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213642
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02595
X-RAY DIFFRACTIONr_mcbond_it1.1291.0051543
X-RAY DIFFRACTIONr_mcbond_other1.0010.9961540
X-RAY DIFFRACTIONr_mcangle_it1.4661.5021958
LS refinement shellResolution: 1.1→1.125 Å
RfactorNum. reflection% reflection
Rfree0.301 149 -
Rwork0.301 11680 -
obs--96.4 %

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