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- PDB-6uo7: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -

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Basic information

Entry
Database: PDB / ID: 6uo7
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) K330L 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 / 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
: / AR-42 / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39501316141 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)40,7355
Polymers40,2791
Non-polymers4564
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-0 kcal/mol
Surface area12940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.000, 60.670, 121.830
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

#1: Protein Histone deacetylase 6


Mass: 40278.570 Da / Num. of mol.: 1 / Mutation: K330L
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
#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.: 2 / Source method: obtained synthetically / Formula: K
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.52 Å3/Da / Density % sol: 51.25 % / 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 magnesium formate dihydrate 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-E / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.39501316141→42.9865271785 Å / Num. obs: 81863 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 11.6388094639 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.032 / Net I/σ(I): 15.2
Reflection shellResolution: 1.4→1.44 Å / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 6.8 / Num. unique obs: 8131 / CC1/2: 0.977 / Rpim(I) all: 0.094

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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: 1.39501316141→42.9865271785 Å / SU ML: 0.114010057186 / Cross valid method: FREE R-VALUE / σ(F): 1.4103068614 / Phase error: 17.8017587333
RfactorNum. reflection% reflection
Rfree0.184402564344 4087 4.99248744854 %
Rwork0.166169430521 --
obs0.167093471164 81863 99.941399812 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 16.2471834664 Å2
Refinement stepCycle: LAST / Resolution: 1.39501316141→42.9865271785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2752 0 26 384 3162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005467407221572952
X-RAY DIFFRACTIONf_angle_d0.8365152193794038
X-RAY DIFFRACTIONf_chiral_restr0.0770374993891445
X-RAY DIFFRACTIONf_plane_restr0.00589214792689531
X-RAY DIFFRACTIONf_dihedral_angle_d21.25214534061072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39501316141-1.41140.2278794953371610.1984987564222693X-RAY DIFFRACTION99.8949947497
1.4114-1.42860.2470621003141250.1945058384512603X-RAY DIFFRACTION99.9633565409
1.4286-1.44670.2335949068651340.1909915155892681X-RAY DIFFRACTION99.9644886364
1.4467-1.46580.2198939280551450.1948888833372624X-RAY DIFFRACTION99.8557518933
1.4658-1.48580.2147759980731350.1935554148182679X-RAY DIFFRACTION99.9644760213
1.4858-1.50710.2142552848781310.1859370379452618X-RAY DIFFRACTION99.9636363636
1.5071-1.52960.2128374212981430.1858173979292673X-RAY DIFFRACTION99.9290276792
1.5296-1.55350.215894072421510.1797924385572619X-RAY DIFFRACTION99.9278499278
1.5535-1.57890.2090304697351540.1733120899912641X-RAY DIFFRACTION99.9284948159
1.5789-1.60620.1956568174291480.1685355517642644X-RAY DIFFRACTION99.7855611151
1.6062-1.63540.1892363788111190.169759471082674X-RAY DIFFRACTION99.6788008565
1.6354-1.66680.1680891072751440.1663123104562672X-RAY DIFFRACTION99.9290276792
1.6668-1.70090.1826519534041310.1671955683362654X-RAY DIFFRACTION100
1.7009-1.73780.1807260451291320.1693667260442672X-RAY DIFFRACTION100
1.7378-1.77830.1618386234511350.1659039808962672X-RAY DIFFRACTION100
1.7783-1.82270.1962986834411350.1680161773592679X-RAY DIFFRACTION100
1.8227-1.8720.176388860831410.1663833299132643X-RAY DIFFRACTION100
1.872-1.92710.1746878505211350.1667432360692670X-RAY DIFFRACTION100
1.9271-1.98930.1954578996431430.1744587303882676X-RAY DIFFRACTION100
1.9893-2.06040.1872797089411180.1703365697452713X-RAY DIFFRACTION100
2.0604-2.14290.1781412954771390.1660942374952664X-RAY DIFFRACTION99.9286987522
2.1429-2.24040.2019805983161480.1659086364812691X-RAY DIFFRACTION100
2.2404-2.35850.1814979570521490.1695906294592687X-RAY DIFFRACTION100
2.3585-2.50630.1917195546691590.1674474839842693X-RAY DIFFRACTION99.9649491763
2.5063-2.69980.1877351678241470.170747380592686X-RAY DIFFRACTION100
2.6998-2.97140.1976366247791450.1674206770412738X-RAY DIFFRACTION100
2.9714-3.40120.1743986398141280.1686536870872767X-RAY DIFFRACTION100
3.4012-4.28460.1655022195631590.1459468251512747X-RAY DIFFRACTION99.8968717772
4.2846-42.98652717850.1572719300941530.1486763024662903X-RAY DIFFRACTION99.7714658831

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