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

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Basic information

Entry
Database: PDB / ID: 6uim
TitleCrystal Structure of Danio rerio Histone Deacetylase 10 in Complex with 7-{[(3-aminopropyl)amino]-2-oxoheptyl} 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 / 7-[(3-aminopropyl)amino]-1-sulfanylheptan-2-one / Polyamine deacetylase HDAC10
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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)75,5947
Polymers75,0421
Non-polymers5526
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-13 kcal/mol
Surface area23440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.871, 80.871, 241.540
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, 20 molecules

#2: Chemical ChemComp-Q7Y / 7-[(3-aminopropyl)amino]-1-sulfanylheptan-2-one


Mass: 218.359 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22N2OS / 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.: 14 / 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: 62.89 %
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 potassium phosphate monobasic, 20% PEG3350, and 0.5% (w/v) n-dodecyl-B-D-maltoside

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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: 2.75→45.73 Å / Num. obs: 24629 / % possible obs: 99.8 % / Redundancy: 8.8 % / Biso Wilson estimate: 67.25 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.085 / Net I/σ(I): 7.2
Reflection shellResolution: 2.75→2.85 Å / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2416 / CC1/2: 0.842 / Rpim(I) all: 0.448

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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: 2.75→45.73 Å / SU ML: 0.412 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.2058
RfactorNum. reflection% reflection
Rfree0.2757 1251 5.09 %
Rwork0.2233 --
obs0.2259 24629 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 72.94 Å2
Refinement stepCycle: LAST / Resolution: 2.75→45.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4692 0 27 14 4733
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00374838
X-RAY DIFFRACTIONf_angle_d0.64366588
X-RAY DIFFRACTIONf_chiral_restr0.0434755
X-RAY DIFFRACTIONf_plane_restr0.0039853
X-RAY DIFFRACTIONf_dihedral_angle_d5.79793908
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.860.4141450.33882541X-RAY DIFFRACTION99.81
2.86-2.990.35931350.29772559X-RAY DIFFRACTION99.74
2.99-3.150.33791440.28792515X-RAY DIFFRACTION99.36
3.15-3.350.37761400.28192577X-RAY DIFFRACTION99.89
3.35-3.60.2511370.25392547X-RAY DIFFRACTION99.85
3.6-3.970.30451340.22632578X-RAY DIFFRACTION99.56
3.97-4.540.24111610.19312582X-RAY DIFFRACTION99.35
4.54-5.720.25851210.19172650X-RAY DIFFRACTION99.64
5.72-40.40.23321340.19642791X-RAY DIFFRACTION99.25

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