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- PDB-6uo3: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -

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Basic information

Entry
Database: PDB / ID: 6uo3
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) complexed with AR-42
ComponentsHDAC6
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 / regulation of tubulin deacetylation / potassium ion binding ...: / Aggrephagy / : / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / histone deacetylase activity / regulation of tubulin deacetylation / 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
: / AR-42 / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09000122285 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: HDAC6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9378
Polymers40,2951
Non-polymers6427
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint8 kcal/mol
Surface area13110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.750, 61.060, 121.650
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 HDAC6 /


Mass: 40294.594 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, 420 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.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-QCP / AR-42 / N-hydroxy-4-{[(2S)-3-methyl-2-phenylbutanoyl]amino}benzamide / Histone deacetylase inhibitor


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.52 Å3/Da / Density % sol: 51.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/ml HDAC6 CD1 2 mM Inhibitor 0.2 M ammonium tartrate dibasic (pH 7.0) 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: Aug 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.09→43.0926147252 Å / Num. obs: 169488 / % possible obs: 99.7 % / Redundancy: 6 % / Biso Wilson estimate: 9.50667468151 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.062 / Net I/σ(I): 7.2
Reflection shellResolution: 1.09→1.12 Å / Rmerge(I) obs: 0.995 / Mean I/σ(I) obs: 2 / Num. unique obs: 16796 / CC1/2: 0.776 / Rpim(I) all: 0.445

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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: 1.09000122285→43.0926147252 Å / SU ML: 0.100731551156 / Cross valid method: FREE R-VALUE / σ(F): 1.33645998405 / Phase error: 19.8872764084
RfactorNum. reflection% reflection
Rfree0.189599042963 8422 4.96908335693 %
Rwork0.183182737462 --
obs0.183501780697 169488 99.615615192 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 14.2140592905 Å2
Refinement stepCycle: LAST / Resolution: 1.09000122285→43.0926147252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 0 38 413 3195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006208482207132974
X-RAY DIFFRACTIONf_angle_d0.8952363000034062
X-RAY DIFFRACTIONf_chiral_restr0.0783286500237442
X-RAY DIFFRACTIONf_plane_restr0.00570315589482537
X-RAY DIFFRACTIONf_dihedral_angle_d21.18808277631066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.09000122285-1.10240.29924473152780.2839543267655306X-RAY DIFFRACTION99.732095017
1.1024-1.11540.2830071197322650.2783003691555346X-RAY DIFFRACTION99.7865907878
1.1154-1.1290.2658511753522710.2625792038695330X-RAY DIFFRACTION99.7151504362
1.129-1.14330.2520674145763180.2606887986865283X-RAY DIFFRACTION99.5733333333
1.1433-1.15830.2718478267052980.2499039112995290X-RAY DIFFRACTION99.9284692418
1.1583-1.17420.2705925060532810.2415646323925355X-RAY DIFFRACTION99.7698707736
1.1742-1.19090.2426058249183020.2345003969225307X-RAY DIFFRACTION99.7332859175
1.1909-1.20870.2355872118952910.2302111185385260X-RAY DIFFRACTION99.7663551402
1.2087-1.22760.2377123691622820.2243928185325353X-RAY DIFFRACTION99.7698300283
1.2276-1.24770.2525589468332970.2164743658325343X-RAY DIFFRACTION99.6642516346
1.2477-1.26930.2316667343642610.2188047065455304X-RAY DIFFRACTION99.4460328806
1.2693-1.29230.207025699073060.2130394570765290X-RAY DIFFRACTION99.5906744972
1.2923-1.31720.2116870079462430.2072728733945369X-RAY DIFFRACTION99.6979925386
1.3172-1.34410.2103253225272830.19817893245353X-RAY DIFFRACTION99.7169143666
1.3441-1.37330.2193488682382820.1985067485055355X-RAY DIFFRACTION99.8052407932
1.3733-1.40530.1875240288922850.1901412365365324X-RAY DIFFRACTION99.786514855
1.4053-1.44040.2075888963012770.1896757510215382X-RAY DIFFRACTION99.5076490241
1.4404-1.47930.1833377011412570.1872682290015353X-RAY DIFFRACTION99.5033699894
1.4793-1.52290.1681379726342690.1789459514765352X-RAY DIFFRACTION99.5219546742
1.5229-1.5720.1798042327762670.1718746515565340X-RAY DIFFRACTION98.9412387507
1.572-1.62820.191202778912920.1656585246065367X-RAY DIFFRACTION99.7883971081
1.6282-1.69340.171468991262440.1714270044335412X-RAY DIFFRACTION99.7882851094
1.6934-1.77050.184191559582610.1699885692885402X-RAY DIFFRACTION99.7007042254
1.7705-1.86380.1772201255912900.1713117614375378X-RAY DIFFRACTION99.6133567663
1.8638-1.98060.1782108414732790.1684506674685361X-RAY DIFFRACTION99.0516332982
1.9806-2.13350.1756258996952700.1636879545125431X-RAY DIFFRACTION99.4938917976
2.1335-2.34820.1664731972982920.1681658136985431X-RAY DIFFRACTION99.5477474343
2.3482-2.6880.1926373736592900.1745836545985457X-RAY DIFFRACTION99.9826026444
2.688-3.38640.1842633195652800.1769456925275570X-RAY DIFFRACTION99.9829089045
3.3864-43.09261472520.1514833384633110.1579269476455662X-RAY DIFFRACTION98.6783413184

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