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- PDB-7kut: Crystal Structure of Danio rerio Histone Deacetylase 10 H137A Mut... -

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Basic information

Entry
Database: PDB / ID: 7kut
TitleCrystal Structure of Danio rerio Histone Deacetylase 10 H137A Mutant in Complex with N-Acetylputrescine (Tetrahedral Intermediate)
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 / 1-[(4-aminobutyl)amino]ethane-1,1-diol / Polyamine deacetylase HDAC10
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)76,53119
Polymers75,1901
Non-polymers1,34118
Water5,927329
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.248, 80.248, 245.960
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: 75189.750 Da / Num. of mol.: 1 / Mutation: H137A
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 , 8 types, 347 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-X51 / 1-[(4-aminobutyl)amino]ethane-1,1-diol


Mass: 148.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H16N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.04 Å3/Da / Density % sol: 59.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL HDAC10, 10 mM Acetylputrescine, 1:1000 trypsin:HDAC10, 0.113 M sodium phosphate monobasic, 0.068 M sodium phosphate dibasic, 18% PEG3350 (w/v), 4% (v/v) polypropylene glycol P400, 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: Feb 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.05→69.5 Å / Num. obs: 58731 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 34.41 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.042 / Net I/σ(I): 11.1
Reflection shellResolution: 2.05→2.11 Å / Rmerge(I) obs: 1.317 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5784 / CC1/2: 0.474 / Rpim(I) all: 0.474

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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: 2.05→60.5 Å / SU ML: 0.2316 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.4469 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2191 2883 4.91 %
Rwork0.1761 55820 -
obs0.1781 58703 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.34 Å2
Refinement stepCycle: LAST / Resolution: 2.05→60.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4843 0 76 329 5248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075060
X-RAY DIFFRACTIONf_angle_d0.85776890
X-RAY DIFFRACTIONf_chiral_restr0.0516792
X-RAY DIFFRACTIONf_plane_restr0.0053884
X-RAY DIFFRACTIONf_dihedral_angle_d8.9224075
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.080.3121230.2562620X-RAY DIFFRACTION99.93
2.08-2.120.31431620.2442581X-RAY DIFFRACTION99.82
2.12-2.160.2621270.23272630X-RAY DIFFRACTION99.93
2.16-2.20.28341300.2252597X-RAY DIFFRACTION99.89
2.2-2.240.26171510.21282636X-RAY DIFFRACTION99.96
2.24-2.290.28341300.20292621X-RAY DIFFRACTION99.89
2.29-2.350.2431600.19542583X-RAY DIFFRACTION99.82
2.35-2.410.24651210.1972644X-RAY DIFFRACTION99.93
2.41-2.470.2819880.20062667X-RAY DIFFRACTION99.96
2.47-2.540.28111420.19482613X-RAY DIFFRACTION99.96
2.54-2.630.27791280.19962661X-RAY DIFFRACTION100
2.63-2.720.22271410.18972642X-RAY DIFFRACTION100
2.72-2.830.22021420.18282635X-RAY DIFFRACTION99.96
2.83-2.960.22141400.17932667X-RAY DIFFRACTION99.96
2.96-3.110.21061330.18392654X-RAY DIFFRACTION100
3.11-3.310.21361150.17972679X-RAY DIFFRACTION100
3.31-3.560.20191570.16562658X-RAY DIFFRACTION100
3.56-3.920.18591360.14962707X-RAY DIFFRACTION100
3.92-4.490.18241470.14462703X-RAY DIFFRACTION99.96
4.49-5.650.20751540.15022727X-RAY DIFFRACTION100
5.65-60.50.20051560.17442895X-RAY DIFFRACTION99.8

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