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

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Basic information

Entry
Database: PDB / ID: 6wsj
TitleCrystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with cyclopeptide des4.3.1
Components
  • Hdac6 protein
  • cyclopeptide des4.3.1
Keywordshydrolase/hydrolase inhibitor / Hydrolase / histone deacetylase / inhibitor / metallohydrolase / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


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 ...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 family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
des4.3.1 / : / Hdac6 protein
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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: Nat Commun / Year: 2021
Title: Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites.
Authors: Hosseinzadeh, P. / Watson, P.R. / Craven, T.W. / Li, X. / Rettie, S. / Pardo-Avila, F. / Bera, A.K. / Mulligan, V.K. / Lu, P. / Ford, A.S. / Weitzner, B.D. / Stewart, L.J. / Moyer, A.P. / Di ...Authors: Hosseinzadeh, P. / Watson, P.R. / Craven, T.W. / Li, X. / Rettie, S. / Pardo-Avila, F. / Bera, A.K. / Mulligan, V.K. / Lu, P. / Ford, A.S. / Weitzner, B.D. / Stewart, L.J. / Moyer, A.P. / Di Piazza, M. / Whalen, J.G. / Greisen, P.J. / Christianson, D.W. / Baker, D.
History
DepositionMay 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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

Downloads & links

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Assembly

Deposited unit
A: Hdac6 protein
I: cyclopeptide des4.3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5507
Polymers41,2832
Non-polymers2685
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-36 kcal/mol
Surface area13110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.500, 84.000, 94.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AI

#1: Protein Hdac6 protein / / Histone Deacetylase 6


Mass: 40285.484 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: A7YT55
#2: Protein/peptide cyclopeptide des4.3.1


Type: Cyclic peptide / Class: Enzyme inhibitor / Mass: 997.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: des4.3.1

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Non-polymers , 4 types, 244 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.53 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL HDAC6 protein 0.2 M ammonium chloride and 20% polyethylene glycol (PEG) 3350 (w/v)

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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: Feb 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→62.76 Å / Num. obs: 45672 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 12.48 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.079 / Net I/σ(I): 9.8
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 45672 / CC1/2: 0.845 / Rpim(I) all: 0.413

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 5EEM

5eem


Resolution: 1.7→62.76 Å / SU ML: 0.1623 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.3393 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1764 2204 4.83 %
Rwork0.154 43453 -
obs0.1551 45657 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.88 Å2
Refinement stepCycle: LAST / Resolution: 1.7→62.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2725 0 79 239 3043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00592897
X-RAY DIFFRACTIONf_angle_d0.9633929
X-RAY DIFFRACTIONf_chiral_restr0.0569429
X-RAY DIFFRACTIONf_plane_restr0.0057512
X-RAY DIFFRACTIONf_dihedral_angle_d8.31852917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.2481120.19512677X-RAY DIFFRACTION99.96
1.74-1.780.21251450.182693X-RAY DIFFRACTION99.96
1.78-1.820.20781220.15442677X-RAY DIFFRACTION99.96
1.82-1.870.19851210.1492685X-RAY DIFFRACTION99.96
1.87-1.930.18031250.14352700X-RAY DIFFRACTION100
1.93-1.990.16771320.14172697X-RAY DIFFRACTION100
1.99-2.060.17591360.15662706X-RAY DIFFRACTION100
2.06-2.140.1781400.14592694X-RAY DIFFRACTION100
2.14-2.240.16461310.14542691X-RAY DIFFRACTION99.93
2.24-2.360.16961600.14492656X-RAY DIFFRACTION100
2.36-2.510.14781442702X-RAY DIFFRACTION100
2.51-2.70.20311430.15672721X-RAY DIFFRACTION99.9
2.7-2.970.18091510.16132717X-RAY DIFFRACTION99.97
2.97-3.40.20041450.16662750X-RAY DIFFRACTION99.9
3.4-4.290.16171280.14882810X-RAY DIFFRACTION100
4.29-62.760.15251690.14882877X-RAY DIFFRACTION99.87

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