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- PDB-7kur: Crystal Structure of Danio rerio Histone Deacetylase 10 Y307F Mut... -

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Basic information

Entry
Database: PDB / ID: 7kur
TitleCrystal Structure of Danio rerio Histone Deacetylase 10 Y307F Mutant in Complex with N-Acetylputrescine
ComponentsPolyamine deacetylase HDAC10
KeywordsHYDROLASE / Histone Deacetylase
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
: / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / N-(4-aminobutyl)acetamide / Polyamine deacetylase HDAC10
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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: 2021
Title: X-ray Crystallographic Snapshots of Substrate Binding in the Active Site of Histone Deacetylase 10.
Authors: Herbst-Gervasoni, C.J. / Christianson, D.W.
History
DepositionNov 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: 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 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyamine deacetylase HDAC10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,92910
Polymers75,2411
Non-polymers6889
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.560, 80.560, 245.710
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: 75240.820 Da / Num. of mol.: 1 / Mutation: Y307F
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 , 7 types, 265 molecules

#2: Chemical ChemComp-X5A / N-(4-aminobutyl)acetamide / N-Acetylputrescine


Mass: 130.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 3.06 Å3/Da / Density % sol: 59.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL HDAC10, 10 mM N-Acetylputrescine, 1:1000 trypsin:HDAC10, 0.100 M sodium phosphate monobasic, 0.100 M sodium phosphate dibasic, 20% PEG3350 (w/v), HDAC10 microseed

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→69.77 Å / Num. obs: 55068 / % possible obs: 100 % / Redundancy: 9.1 % / Biso Wilson estimate: 35.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.039 / Net I/σ(I): 11.8
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 1.026 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5481 / CC1/2: 0.684 / Rpim(I) all: 0.356

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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: 2.1→69.77 Å / SU ML: 0.2281 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3812 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2174 2701 4.91 %
Rwork0.1906 52357 -
obs0.192 55058 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.03 Å2
Refinement stepCycle: LAST / Resolution: 2.1→69.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4844 0 35 256 5135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00685002
X-RAY DIFFRACTIONf_angle_d0.87086809
X-RAY DIFFRACTIONf_chiral_restr0.0498781
X-RAY DIFFRACTIONf_plane_restr0.0055875
X-RAY DIFFRACTIONf_dihedral_angle_d7.90344061
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.34931140.292763X-RAY DIFFRACTION100
2.14-2.180.28991470.26422713X-RAY DIFFRACTION100
2.18-2.220.3061450.25862691X-RAY DIFFRACTION100
2.22-2.270.31811490.22952664X-RAY DIFFRACTION99.89
2.27-2.330.26141370.23292738X-RAY DIFFRACTION100
2.33-2.380.25571400.21362713X-RAY DIFFRACTION100
2.38-2.450.25351240.20952777X-RAY DIFFRACTION99.93
2.45-2.520.25671360.20762731X-RAY DIFFRACTION100
2.52-2.60.24261320.20512727X-RAY DIFFRACTION100
2.6-2.690.24891430.19872739X-RAY DIFFRACTION100
2.69-2.80.21891290.19952730X-RAY DIFFRACTION100
2.8-2.930.25691440.21252729X-RAY DIFFRACTION99.97
2.93-3.080.22781340.21912765X-RAY DIFFRACTION100
3.08-3.280.25121310.21572769X-RAY DIFFRACTION100
3.28-3.530.22641550.19542747X-RAY DIFFRACTION99.86
3.53-3.890.19661710.16942764X-RAY DIFFRACTION99.97
3.89-4.450.18781700.15292783X-RAY DIFFRACTION99.93
4.45-5.60.1681530.15042824X-RAY DIFFRACTION100
5.6-69.770.18211470.17562990X-RAY DIFFRACTION99.37

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