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- PDB-6uo5: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -

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Basic information

Entry
Database: PDB / ID: 6uo5
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) Y363F mutant complexed with AR-42
ComponentsHistone deacetylase 6
KeywordsHydrolase/Hydrolase Inhibitor / Histone Deacetylase / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


Aggrephagy / 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 ...Aggrephagy / 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 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
: / AR-42 / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43934220419 Å
AuthorsOsko, J.D. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM49758 United States
CitationJournal: Biochemistry / Year: 2019
Title: Structural Basis of Catalysis and Inhibition of HDAC6 CD1, the Enigmatic Catalytic Domain of Histone Deacetylase 6.
Authors: Osko, J.D. / Christianson, D.W.
History
DepositionOct 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7976
Polymers40,2791
Non-polymers5185
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint4 kcal/mol
Surface area12870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.569, 60.546, 121.972
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, 1 molecules A

#1: Protein Histone deacetylase 6


Mass: 40278.594 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 , 5 types, 267 molecules

#2: Chemical ChemComp-QCP / AR-42 / N-hydroxy-4-{[(2S)-3-methyl-2-phenylbutanoyl]amino}benzamide


Mass: 312.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N2O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.5 Å3/Da / Density % sol: 50.82 % / Description: Perfect Diamond Shape
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/ml HDAC6 CD1 2 mM Inhibitor 0.2 M sodium phosphate dibasic dihydride 20% PEG 3350 1:1 ratio protein to precipitant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.43934220419→60.986 Å / Num. obs: 73858 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 16.1241389087 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.022 / Net I/σ(I): 19.2
Reflection shellResolution: 1.44→1.49 Å / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7242 / CC1/2: 0.872 / Rpim(I) all: 0.316

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EEF

5eef


Resolution: 1.43934220419→60.986 Å / SU ML: 0.14875581832 / Cross valid method: FREE R-VALUE / σ(F): 1.34759331692 / Phase error: 20.1078632787
RfactorNum. reflection% reflection
Rfree0.196514475533 3692 4.99878144548 %
Rwork0.174069590833 --
obs0.17517285659 73858 99.8027133668 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.6594621011 Å2
Refinement stepCycle: LAST / Resolution: 1.43934220419→60.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2746 0 30 262 3038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005630496850042924
X-RAY DIFFRACTIONf_angle_d0.8184841221283991
X-RAY DIFFRACTIONf_chiral_restr0.0765546822191442
X-RAY DIFFRACTIONf_plane_restr0.00581156275456522
X-RAY DIFFRACTIONf_dihedral_angle_d21.62217148171050
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43934220419-1.45830.2944665346871380.2701433228672627X-RAY DIFFRACTION98.855917054
1.4583-1.47830.266155488361510.2608700335182685X-RAY DIFFRACTION99.8591549296
1.4783-1.49940.2739046694091380.2327599103972616X-RAY DIFFRACTION99.7464686708
1.4994-1.52180.2515107364031250.2316498425772700X-RAY DIFFRACTION99.6472663139
1.5218-1.54550.2303014849161320.2173477679222666X-RAY DIFFRACTION99.7860199715
1.5455-1.57090.2580729720011460.2156785272072655X-RAY DIFFRACTION99.8218104063
1.5709-1.5980.2419872888081290.1991679070152711X-RAY DIFFRACTION99.9648011264
1.598-1.6270.1899727385331520.1896478085512639X-RAY DIFFRACTION99.9283924096
1.627-1.65830.2292336891611490.1914267271392670X-RAY DIFFRACTION100
1.6583-1.69220.2199605584671310.1960260598872682X-RAY DIFFRACTION99.9644633973
1.6922-1.7290.200319189931160.1957975873522717X-RAY DIFFRACTION99.9294532628
1.729-1.76920.2281170487081400.1935625713962686X-RAY DIFFRACTION99.8939554613
1.7692-1.81340.210380538121450.1840814573212666X-RAY DIFFRACTION99.9644381223
1.8134-1.86250.234538619641510.1863192136982669X-RAY DIFFRACTION99.9645515775
1.8625-1.91730.2096440385281650.1810389389742651X-RAY DIFFRACTION99.8935792834
1.9173-1.97920.2067066476481540.181880631792687X-RAY DIFFRACTION99.4399719986
1.9792-2.04990.1803211399491180.1739733061922707X-RAY DIFFRACTION99.9292536258
2.0499-2.1320.1828883496571120.1741431451192721X-RAY DIFFRACTION100
2.132-2.2290.1763954567491750.1701204372252679X-RAY DIFFRACTION99.9649737303
2.229-2.34660.1950131684991690.1738909306062692X-RAY DIFFRACTION99.8603839442
2.3466-2.49360.1859319688381420.1736523167162719X-RAY DIFFRACTION99.8952513966
2.4936-2.68610.1987750559291330.1746574216012722X-RAY DIFFRACTION99.5120250959
2.6861-2.95640.1877335664751300.1743757860382745X-RAY DIFFRACTION99.6188496188
2.9564-3.38420.1915227678221560.1664120561782756X-RAY DIFFRACTION99.9656711294
3.3842-4.26360.1819909357911460.1513135986012781X-RAY DIFFRACTION99.9658469945
4.2636-60.9860.1752175765111490.150100232892917X-RAY DIFFRACTION99.5777849951

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