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

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Basic information

Entry
Database: PDB / ID: 6wyo
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) H82F F202Y double mutant complexed with Trichostatin A
ComponentsHistone deacetylase 6
KeywordsHYDROLASE / Histone Deacetylase / metalloprotein
Function / homology
Function and homology information


negative regulation of cellular component organization / positive regulation of cellular component organization / Aggrephagy / regulation of biological quality / deacetylase activity / tubulin deacetylase activity / mitochondrion localization / swimming behavior / definitive hemopoiesis / regulation of microtubule-based process ...negative regulation of cellular component organization / positive regulation of cellular component organization / Aggrephagy / regulation of biological quality / deacetylase activity / tubulin deacetylase activity / mitochondrion localization / swimming behavior / definitive hemopoiesis / regulation of microtubule-based process / protein lysine deacetylase activity / response to stress / potassium ion binding / hematopoietic progenitor cell differentiation / transferase activity / actin binding / chromatin organization / angiogenesis / perikaryon / axon / dendrite / centrosome / zinc ion binding / nucleus / cytoplasm / cytosol
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 family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
: / TRICHOSTATIN A / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.30000278768 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: Acta Crystallogr.,Sect.F / Year: 2020
Title: Binding of inhibitors to active-site mutants of CD1, the enigmatic catalytic domain of histone deacetylase 6.
Authors: Osko, J.D. / Christianson, D.W.
History
DepositionMay 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone deacetylase 6
B: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,04710
Polymers84,1552
Non-polymers8928
Water2,090116
1
A: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5245
Polymers42,0781
Non-polymers4464
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5245
Polymers42,0781
Non-polymers4464
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.087, 123.993, 55.012
Angle α, β, γ (deg.)90.000, 114.421, 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 Histone deacetylase 6


Mass: 42077.652 Da / Num. of mol.: 2 / Mutation: H82F,F202Y
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.04 Å3/Da / Density % sol: 39.84 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL HDAC6 Protein 0.2 M Potassium acetate 20% peg 3350 1:1 ratio protein to precipitant solution

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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: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→50.1 Å / Num. obs: 28350 / % possible obs: 98.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 32.5564079678 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.052 / Net I/σ(I): 8.9
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.418 / Num. unique obs: 2842 / CC1/2: 0.792 / Rpim(I) all: 0.395 / % possible all: 98.4

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Processing

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

5eef


Resolution: 2.30000278768→50.090196779 Å / SU ML: 0.29965551381 / Cross valid method: FREE R-VALUE / σ(F): 1.38501881023 / Phase error: 24.0334206853
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.231983322559 1473 5.19576719577 %
Rwork0.170581866721 26877 -
obs0.173674284168 28350 98.5435712051 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.0078730162 Å2
Refinement stepCycle: LAST / Resolution: 2.30000278768→50.090196779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5276 0 50 116 5442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007325370597045462
X-RAY DIFFRACTIONf_angle_d0.9039649612497440
X-RAY DIFFRACTIONf_chiral_restr0.0504531411741836
X-RAY DIFFRACTIONf_plane_restr0.0055723465874967
X-RAY DIFFRACTIONf_dihedral_angle_d6.636419407234324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3000028-2.37420.2790285750791510.209747737072414X-RAY DIFFRACTION99.2263056093
2.3742-2.45910.2838254340851600.196189228522432X-RAY DIFFRACTION99.196326062
2.4591-2.55750.300032437557990.1959351210932497X-RAY DIFFRACTION99.4255074684
2.5575-2.67390.2879049782571210.193483020022459X-RAY DIFFRACTION98.9643268124
2.6739-2.81490.2291266913351280.1873345959332434X-RAY DIFFRACTION98.0107115532
2.8149-2.99120.2880463099911440.1907673550882416X-RAY DIFFRACTION98.8035507526
2.9912-3.22220.2473588857311370.1783929321932470X-RAY DIFFRACTION99.0125332321
3.2222-3.54630.2174816516941260.1747553765992473X-RAY DIFFRACTION99.3881453155
3.5463-4.05930.2141858852051240.1513731300692417X-RAY DIFFRACTION97.3563218391
4.0593-5.11350.2016962088681410.1441406046782427X-RAY DIFFRACTION97.8285714286
5.1135-50.090.1995754121971420.1643326362882438X-RAY DIFFRACTION96.8105065666

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