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

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Basic information

Entry
Database: PDB / ID: 6ufo
TitleCrystal Structure of Danio rerio Histone Deacetylase 10 in Complex with 7-[(3-aminopropyl)amino]-1-methoxyheptan-2-one
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 / Chem-Q6P / Polyamine deacetylase HDAC10
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 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
DepositionSep 24, 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 / 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.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)75,7048
Polymers75,0421
Non-polymers6637
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-20 kcal/mol
Surface area23470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.850, 80.850, 247.025
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 / Histone deacetylase 10


Mass: 75041.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac10 / Production host: Escherichia coli (E. coli)
References: UniProt: F1QCV2, acetylspermidine deacetylase, acetylputrescine deacetylase

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Non-polymers , 5 types, 62 molecules

#2: Chemical ChemComp-Q6P / 7-[(3-aminopropyl)amino]-1-methoxyheptane-2,2-diol


Mass: 234.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O3 / 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.: 3 / 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.: 55 / 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: 3.27 Å3/Da / Density % sol: 62.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL zHDAC10, 5 mM inhibitor 3, 1:1000 trypsin:zHDAC10, 0.1 M potassium phosphate monobasic, 0.1 M potassium phosphate dibasic, 20% PEG3350, seeded with zHDAC10 microcrystals, one hour at room temperature

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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: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 5, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.68→28.84 Å / Num. obs: 27000 / % possible obs: 99.7 % / Redundancy: 9.9 % / Biso Wilson estimate: 56.3 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.073 / Net I/σ(I): 10.5
Reflection shellResolution: 2.68→2.78 Å / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2553 / CC1/2: 0.806 / Rpim(I) all: 0.421

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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 5TD7

5td7


Resolution: 2.68→28.84 Å / SU ML: 0.3371 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.1856
RfactorNum. reflection% reflection
Rfree0.2346 2003 7.42 %
Rwork0.1946 --
obs0.1975 26997 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 55.22 Å2
Refinement stepCycle: LAST / Resolution: 2.68→28.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4852 0 34 55 4941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025013
X-RAY DIFFRACTIONf_angle_d0.49926827
X-RAY DIFFRACTIONf_chiral_restr0.04780
X-RAY DIFFRACTIONf_plane_restr0.0037878
X-RAY DIFFRACTIONf_dihedral_angle_d6.28854064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.750.32591270.27081656X-RAY DIFFRACTION94.59
2.75-2.820.35711450.25151751X-RAY DIFFRACTION100
2.82-2.910.30541400.23611744X-RAY DIFFRACTION99.95
2.91-30.31851430.23531775X-RAY DIFFRACTION100
3-3.110.29111390.24181794X-RAY DIFFRACTION100
3.11-3.230.29091440.24781761X-RAY DIFFRACTION100
3.23-3.380.27521400.23341761X-RAY DIFFRACTION100
3.38-3.560.25821400.20621776X-RAY DIFFRACTION100
3.56-3.780.22881480.1881773X-RAY DIFFRACTION100
3.78-4.070.19841410.17821795X-RAY DIFFRACTION100
4.07-4.480.19591470.15861806X-RAY DIFFRACTION100
4.48-5.120.20471440.1521807X-RAY DIFFRACTION100
5.12-6.440.22811490.19561846X-RAY DIFFRACTION100
6.44-28.840.19581560.18071949X-RAY DIFFRACTION99.72

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