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

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Basic information

Entry
Database: PDB / ID: 7kus
TitleCrystal Structure of Danio rerio Histone Deacetylase 10 H137A Mutant in Complex with N8-Acetylspermidine (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 / Chem-X54 / Polyamine deacetylase HDAC10
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.3Oct 23, 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)76,19312
Polymers75,1901
Non-polymers1,00311
Water5,801322
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)80.489, 80.489, 245.308
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 , 7 types, 333 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-X54 / 1-({4-[(3-aminopropyl)amino]butyl}amino)ethane-1,1-diol


Mass: 205.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H23N3O2 / Feature type: SUBJECT OF INVESTIGATION
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL HDAC10, 10 mM N8-Acetylspermidine, 1:1000 trypsin:HDAC10, 0.113 M sodium phosphate monobasic, 0.068 M sodium phosphate dibasic, 18% PEG3350 (w/v), 3% (w/v) 1,5-Diaminopentane ...Details: 10 mg/mL HDAC10, 10 mM N8-Acetylspermidine, 1:1000 trypsin:HDAC10, 0.113 M sodium phosphate monobasic, 0.068 M sodium phosphate dibasic, 18% PEG3350 (w/v), 3% (w/v) 1,5-Diaminopentane dihydrochloride, 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→69.71 Å / Num. obs: 62900 / % possible obs: 99.4 % / Redundancy: 9.4 % / Biso Wilson estimate: 35.22 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.039 / Net I/σ(I): 10.5
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 1.104 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 6197 / CC1/2: 0.604 / Rpim(I) all: 0.393

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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→60.6 Å / SU ML: 0.1867 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.5651 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2122 3106 4.94 %
Rwork0.1749 59768 -
obs0.1767 62874 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.7 Å2
Refinement stepCycle: LAST / Resolution: 2→60.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4856 0 55 322 5233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00665092
X-RAY DIFFRACTIONf_angle_d0.86196941
X-RAY DIFFRACTIONf_chiral_restr0.0515794
X-RAY DIFFRACTIONf_plane_restr0.0056891
X-RAY DIFFRACTIONf_dihedral_angle_d7.62664135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.29091490.25072658X-RAY DIFFRACTION99.26
2.03-2.060.29021450.24272709X-RAY DIFFRACTION99.37
2.06-2.10.27371050.24622655X-RAY DIFFRACTION98.5
2.1-2.140.27151360.23272590X-RAY DIFFRACTION96.16
2.14-2.180.27131390.22062701X-RAY DIFFRACTION99.44
2.18-2.220.25741250.21312691X-RAY DIFFRACTION99.44
2.22-2.270.22771500.20022651X-RAY DIFFRACTION99.43
2.27-2.330.24041210.19512733X-RAY DIFFRACTION99.51
2.33-2.380.21361850.18992616X-RAY DIFFRACTION99.47
2.38-2.450.21751160.18652768X-RAY DIFFRACTION99.72
2.45-2.520.20991490.18222699X-RAY DIFFRACTION99.62
2.52-2.60.24571530.18822692X-RAY DIFFRACTION99.65
2.6-2.690.24221500.18682714X-RAY DIFFRACTION99.65
2.69-2.80.23031580.19412675X-RAY DIFFRACTION99.79
2.8-2.930.25361370.19392738X-RAY DIFFRACTION99.76
2.93-3.080.23071340.192662X-RAY DIFFRACTION96.95
3.08-3.280.24271500.1822726X-RAY DIFFRACTION99.65
3.28-3.530.21971370.17752760X-RAY DIFFRACTION100
3.53-3.890.20071350.15422776X-RAY DIFFRACTION100
3.89-4.450.16321430.1382816X-RAY DIFFRACTION100
4.45-5.60.16231540.14152805X-RAY DIFFRACTION99.97
5.6-60.60.18371350.1652933X-RAY DIFFRACTION97.49

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