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- PDB-6uij: Crystal Structure of Danio rerio Histone Deacetylase 10 in Comple... -

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Basic information

Entry
Database: PDB / ID: 6uij
TitleCrystal Structure of Danio rerio Histone Deacetylase 10 in Complex with S-{5-[(3-aminopropyl)amino]pentyl} thioacetate
ComponentsPolyamine deacetylase HDAC10
KeywordsHydrolase/Hydrolase Inhibitor / Histone Deacetylase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


polyamine deacetylation / spermidine deacetylation / HDACs deacetylate histones / acetylspermidine deacetylase / acetylspermidine deacetylase activity / acetylputrescine deacetylase / acetylputrescine deacetylase activity / deacetylase activity / homologous recombination / swimming behavior ...polyamine deacetylation / spermidine deacetylation / HDACs deacetylate histones / acetylspermidine deacetylase / acetylspermidine deacetylase activity / acetylputrescine deacetylase / acetylputrescine deacetylase activity / deacetylase activity / homologous recombination / swimming behavior / epigenetic regulation of gene expression / macroautophagy / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
: / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily
Similarity search - Domain/homology
: / PHOSPHATE ION / 5-[(3-aminopropyl)amino]pentane-1-thiol / Polyamine deacetylase HDAC10
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHerbst-Gervasoni, C.J. / 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: Binding ofN8-Acetylspermidine Analogues to Histone Deacetylase 10 Reveals Molecular Strategies for Blocking Polyamine Deacetylation.
Authors: Herbst-Gervasoni, C.J. / Christianson, D.W.
History
DepositionOct 1, 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.title / _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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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: Polyamine deacetylase HDAC10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5517
Polymers75,0421
Non-polymers5106
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-12 kcal/mol
Surface area22440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.780, 80.780, 242.602
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Polyamine deacetylase HDAC10


Mass: 75041.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Production host: Escherichia coli (E. coli)
References: UniProt: F1QCV2, acetylspermidine deacetylase, acetylputrescine deacetylase

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Non-polymers , 5 types, 24 molecules

#2: Chemical ChemComp-SS9 / 5-[(3-aminopropyl)amino]pentane-1-thiol


Mass: 176.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H20N2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.31 Å3/Da / Density % sol: 62.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL zHDAC10, 5 mM inhibitor 2, 1:1000 trypsin:zHDAC10, 0.2 M ammonium phosphate monobasic, 20% PEG3350, and 4% (v/v) 1-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.9→45.83 Å / Num. obs: 21155 / % possible obs: 99.9 % / Redundancy: 8.8 % / Biso Wilson estimate: 72.97 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.084 / Net I/σ(I): 10.4
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 1.63 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2088 / CC1/2: 0.512 / Rpim(I) all: 0.853

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5td7

5td7


Resolution: 2.9→45.83 Å / SU ML: 0.475 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.3943
RfactorNum. reflection% reflection
Rfree0.2492 1110 5.25 %
Rwork0.2029 --
obs0.2055 21153 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 72.95 Å2
Refinement stepCycle: LAST / Resolution: 2.9→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4681 0 24 18 4723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514819
X-RAY DIFFRACTIONf_angle_d0.77696562
X-RAY DIFFRACTIONf_chiral_restr0.0476754
X-RAY DIFFRACTIONf_plane_restr0.0053848
X-RAY DIFFRACTIONf_dihedral_angle_d5.84263887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.030.37881240.31812455X-RAY DIFFRACTION100
3.03-3.190.33861320.28192477X-RAY DIFFRACTION99.73
3.19-3.390.35181510.27042442X-RAY DIFFRACTION100
3.39-3.650.29821350.22972476X-RAY DIFFRACTION100
3.65-4.020.26271240.2022497X-RAY DIFFRACTION99.7
4.02-4.60.22261310.16672488X-RAY DIFFRACTION100
4.6-5.80.21771300.17292570X-RAY DIFFRACTION99.96
5.8-45.830.2061830.1822638X-RAY DIFFRACTION99.75

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