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- PDB-8eqi: Crystal Structure of Danio rerio histone deacetylase 6 catalytic ... -

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Basic information

Entry
Database: PDB / ID: 8eqi
TitleCrystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with cyclopeptide des4.2.0
Components
  • Cyclopeptide des4.2.0
  • Hdac6 protein
KeywordsHYDROLASE/INHIBITOR / Hydrolase / histone deacetylase / inhibitor / metallohydrolase / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


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 ...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 family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Biological speciesDanio rerio (zebrafish)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWatson, P.R. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM49758 United States
CitationJournal: Acs Chem.Biol. / Year: 2023
Title: Macrocyclic Octapeptide Binding and Inferences on Protein Substrate Binding to Histone Deacetylase 6.
Authors: Watson, P.R. / Gupta, S. / Hosseinzadeh, P. / Brown, B.P. / Baker, D. / Christianson, D.W.
History
DepositionOct 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: 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 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.details
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hdac6 protein
B: Hdac6 protein
F: Cyclopeptide des4.2.0
G: Cyclopeptide des4.2.0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,88810
Polymers82,6014
Non-polymers2876
Water5,278293
1
A: Hdac6 protein
F: Cyclopeptide des4.2.0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4445
Polymers41,3012
Non-polymers1443
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-42 kcal/mol
Surface area12790 Å2
MethodPISA
2
B: Hdac6 protein
G: Cyclopeptide des4.2.0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4445
Polymers41,3012
Non-polymers1443
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-43 kcal/mol
Surface area13100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.450, 92.030, 153.200
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 Hdac6 protein / Histone Deacetylase 6


Mass: 40285.484 Da / Num. of mol.: 2 / Fragment: catalytic domain 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: A7YT55
#2: Protein/peptide Cyclopeptide des4.2.0


Mass: 1015.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.45 Å3/Da / Density % sol: 49.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100nL of 10mg/mL HDAC6 with 100nL precipitant (0.2 M ammonium tartrate dibasic pH 7.0, 20% w/v polyethylene glycol 3,350) followed by 25 nL of precipitant solution containing crystal seeds ...Details: 100nL of 10mg/mL HDAC6 with 100nL precipitant (0.2 M ammonium tartrate dibasic pH 7.0, 20% w/v polyethylene glycol 3,350) followed by 25 nL of precipitant solution containing crystal seeds of the HDAC6 complex with octapeptide inhibitor des4.3.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→78.89 Å / Num. obs: 111093 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 14.16 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.256 / Rpim(I) all: 0.115 / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 1.037 / Num. unique obs: 10837 / CC1/2: 0.61 / Rpim(I) all: 0.471

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Zanudadata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB: 5EEM

5eem


Resolution: 2→78.89 Å / SU ML: 0.1997 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.2824
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2721 2820 5.08 %
Rwork0.2355 52713 -
obs0.2374 55533 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.16 Å2
Refinement stepCycle: LAST / Resolution: 2→78.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5398 0 144 293 5835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00735675
X-RAY DIFFRACTIONf_angle_d0.93097707
X-RAY DIFFRACTIONf_chiral_restr0.0542847
X-RAY DIFFRACTIONf_plane_restr0.00951004
X-RAY DIFFRACTIONf_dihedral_angle_d21.6986780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.28861500.26062556X-RAY DIFFRACTION99.52
2.03-2.070.29511460.24772575X-RAY DIFFRACTION99.67
2.07-2.110.3251300.24422608X-RAY DIFFRACTION99.78
2.11-2.150.28181290.25312640X-RAY DIFFRACTION99.57
2.15-2.20.30761330.23872589X-RAY DIFFRACTION99.63
2.2-2.250.29441500.23792593X-RAY DIFFRACTION99.75
2.25-2.310.26511390.2352621X-RAY DIFFRACTION99.64
2.31-2.370.28021450.23312596X-RAY DIFFRACTION99.85
2.37-2.440.29371360.23072617X-RAY DIFFRACTION99.75
2.44-2.520.26121300.23232629X-RAY DIFFRACTION99.64
2.52-2.610.25321250.23072642X-RAY DIFFRACTION99.75
2.61-2.710.26821350.23832640X-RAY DIFFRACTION99.82
2.71-2.840.28911380.24312622X-RAY DIFFRACTION99.86
2.84-2.990.32421360.24052628X-RAY DIFFRACTION99.78
2.99-3.170.30571480.24842657X-RAY DIFFRACTION99.79
3.17-3.420.22061350.24982657X-RAY DIFFRACTION99.79
3.42-3.760.28121360.22992654X-RAY DIFFRACTION99.75
3.76-4.310.25581520.20662674X-RAY DIFFRACTION99.86
4.31-5.430.20071610.21292715X-RAY DIFFRACTION99.65
5.43-78.890.28111660.24872800X-RAY DIFFRACTION98.64

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