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- PDB-6uo2: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -

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Basic information

Entry
Database: PDB / ID: 6uo2
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) complexed with Trichostatin A
ComponentsHDAC6
KeywordsHYDROLASE / Histone Deacetylase
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
: / TRICHOSTATIN A / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65002315533 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 / 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_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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

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Assembly

Deposited unit
A: HDAC6
B: HDAC6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,48110
Polymers80,5892
Non-polymers8928
Water3,477193
1
A: HDAC6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7415
Polymers40,2951
Non-polymers4464
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HDAC6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7415
Polymers40,2951
Non-polymers4464
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.030, 124.261, 55.520
Angle α, β, γ (deg.)90.000, 114.090, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein HDAC6


Mass: 40294.594 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: 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.: 2 / Source method: obtained synthetically / Formula: C17H22N2O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: antifungal, antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.07 Å3/Da / Density % sol: 40.64 % / 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 ammonium tartrate dibasic (pH 7.0) 20% PEG 3350 1:1 protein precipitant drop ratio

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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: 1.65→50.6846920791 Å / Num. obs: 77846 / % possible obs: 99.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 20.2932988515 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.041 / Net I/σ(I): 9.9
Reflection shellResolution: 1.65→1.7 Å / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 2 / Num. unique obs: 7694 / CC1/2: 0.753 / Rpim(I) all: 0.35

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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: 1.65002315533→50.6846920791 Å / SU ML: 0.186776196696 / Cross valid method: FREE R-VALUE / σ(F): 1.35058941455 / Phase error: 22.9253919588
RfactorNum. reflection% reflection
Rfree0.222436905036 3963 5.09082033759 %
Rwork0.187287681155 --
obs0.189023392601 77846 99.0356724849 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.3808006679 Å2
Refinement stepCycle: LAST / Resolution: 1.65002315533→50.6846920791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5400 0 50 193 5643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005572072801825656
X-RAY DIFFRACTIONf_angle_d0.8007520645917711
X-RAY DIFFRACTIONf_chiral_restr0.0515896958355850
X-RAY DIFFRACTIONf_plane_restr0.005342924915891011
X-RAY DIFFRACTIONf_dihedral_angle_d15.8527266183317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65002315533-1.67010.305285018511420.2719453391732554X-RAY DIFFRACTION98.4300839723
1.6701-1.69130.3082742767311350.2678080591172674X-RAY DIFFRACTION98.5614035088
1.6913-1.71350.3075330948961520.2607255335572593X-RAY DIFFRACTION98.3870967742
1.7135-1.7370.2825980330461510.2452041127682611X-RAY DIFFRACTION98.8193202147
1.737-1.76180.2756529517661470.2351520429042575X-RAY DIFFRACTION98.1962481962
1.7618-1.78810.2921166583311550.2300406655212599X-RAY DIFFRACTION96.8014059754
1.7881-1.81610.2696305775331290.2236549165212623X-RAY DIFFRACTION98.7796123475
1.8161-1.84590.2711973679241570.2158068403582642X-RAY DIFFRACTION99.5376955903
1.8459-1.87770.2508045429471430.2168712250622606X-RAY DIFFRACTION99.6736765772
1.8777-1.91180.276129399071690.2130718779822652X-RAY DIFFRACTION99.3659739345
1.9118-1.94860.2901491415891490.2168031025792617X-RAY DIFFRACTION99.4964028777
1.9486-1.98840.2230378997661530.2084493434622642X-RAY DIFFRACTION99.537037037
1.9884-2.03160.2660487229071510.2067723554672661X-RAY DIFFRACTION99.4342291372
2.0316-2.07890.2436687594541480.2020671214052620X-RAY DIFFRACTION99.4252873563
2.0789-2.13090.2135963807771410.1984028885482632X-RAY DIFFRACTION98.9650249822
2.1309-2.18850.2104522624451140.1953506374812667X-RAY DIFFRACTION98.8975817923
2.1885-2.25290.2024091933361130.1946903143162651X-RAY DIFFRACTION99.317283507
2.2529-2.32560.2233522498281340.1924221250072667X-RAY DIFFRACTION99.0802971348
2.3256-2.40870.2229113724411490.1956288770442646X-RAY DIFFRACTION99.0432317505
2.4087-2.50510.2368134206161360.1982184883732580X-RAY DIFFRACTION97.3825743994
2.5051-2.61920.2537732605761410.199214385682630X-RAY DIFFRACTION98.7174919843
2.6192-2.75720.2243247890621240.1918432313682681X-RAY DIFFRACTION99.8931623932
2.7572-2.930.239210196208990.1950997222862731X-RAY DIFFRACTION99.9293785311
2.93-3.15620.2156916627941230.1955698062172667X-RAY DIFFRACTION99.8925886144
3.1562-3.47370.2137430193871760.1843730043472657X-RAY DIFFRACTION99.8942172073
3.4737-3.97620.2028273244541420.159371878252660X-RAY DIFFRACTION99.5735607676
3.9762-5.00890.1620947251541310.1390038310162648X-RAY DIFFRACTION98.2673267327
5.0089-50.68469207910.182935152971590.154211547352697X-RAY DIFFRACTION99.7206703911

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