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

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Basic information

Entry
Database: PDB / ID: 6cgp
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with MAIP-032
ComponentsHdac6 protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Histone deacetylase / metallohydrolase / HYDROLASE-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 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
Chem-F1Y / : / Hdac6 protein
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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: Org. Lett. / Year: 2018
Title: Multicomponent Synthesis and Binding Mode of Imidazo[1,2- a]pyridine-Capped Selective HDAC6 Inhibitors.
Authors: Mackwitz, M.K.W. / Hamacher, A. / Osko, J.D. / Held, J. / Scholer, A. / Christianson, D.W. / Kassack, M.U. / Hansen, F.K.
History
DepositionFeb 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
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
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8026
Polymers40,2851
Non-polymers5165
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint2 kcal/mol
Surface area12790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.310, 64.950, 140.499
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hdac6 protein / histone deacetylase 6


Mass: 40285.484 Da / Num. of mol.: 1 / Fragment: catalytic domain 2 (UNP residues 288-646)
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

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Non-polymers , 5 types, 19 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-F1Y / N-hydroxy-4-[(2-propylimidazo[1,2-a]pyridin-3-yl)amino]benzamide


Mass: 310.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18N4O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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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: 2.56 Å3/Da / Density % sol: 55 % / Description: Thin needle-like crystals
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10 mg/mL ZCD2, MES, pH 6.0, 14% w/v PEG4000, crystals appeared within 2 days
Temp details: The crystal trays were never removed from this temperature.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2017
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→70.25 Å / Num. obs: 14843 / % possible obs: 99.3 % / Redundancy: 4.8 % / CC1/2: 0.988 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.109 / Net I/σ(I): 5.7
Reflection shellResolution: 2.5→2.59 Å / Num. unique obs: 7253 / CC1/2: 0.476 / Rpim(I) all: 0.782

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5EEM

5eem


Resolution: 2.5→38.077 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.97
RfactorNum. reflection% reflection
Rfree0.2664 661 4.46 %
Rwork0.2132 --
obs0.2155 14821 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→38.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2739 0 30 14 2783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022837
X-RAY DIFFRACTIONf_angle_d0.73856
X-RAY DIFFRACTIONf_dihedral_angle_d9.3681668
X-RAY DIFFRACTIONf_chiral_restr0.043422
X-RAY DIFFRACTIONf_plane_restr0.005503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.6930.35241220.31752762X-RAY DIFFRACTION98
2.693-2.96390.3421360.29852777X-RAY DIFFRACTION100
2.9639-3.39260.341520.26452770X-RAY DIFFRACTION99
3.3926-4.27340.27181070.19442876X-RAY DIFFRACTION99
4.2734-38.0810.18771440.15462975X-RAY DIFFRACTION99

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