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

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Basic information

Entry
Database: PDB / ID: 6vnq
TitleCrystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Bishydroxamic Acid Based Inhibitor
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 ...polyamine deacetylation / spermidine deacetylation / HDACs deacetylate histones / : / acetylspermidine deacetylase / acetylspermidine deacetylase activity / acetylputrescine deacetylase / acetylputrescine deacetylase activity / deacetylase activity / homologous recombination / swimming behavior / regulation of tubulin deacetylation / macroautophagy / negative regulation of transcription by RNA polymerase II / 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-R5G / 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: Chemmedchem / Year: 2020
Title: Design and Synthesis of Dihydroxamic Acids as HDAC6/8/10 Inhibitors.
Authors: Morgen, M. / Steimbach, R.R. / Geraldy, M. / Hellweg, L. / Sehr, P. / Ridinger, J. / Witt, O. / Oehme, I. / Herbst-Gervasoni, C.J. / Osko, J.D. / Porter, N.J. / Christianson, D.W. / Gunkel, N. / Miller, A.K.
History
DepositionJan 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
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)75,8399
Polymers75,0561
Non-polymers7838
Water4,702261
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-10 kcal/mol
Surface area23300 Å2
Unit cell
Length a, b, c (Å)80.549, 80.549, 245.370
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: 75055.641 Da / Num. of mol.: 1 / Mutation: A24E,D94A
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 , 6 types, 269 molecules

#2: Chemical ChemComp-R5G / N-hydroxy-1-{[4-(hydroxycarbamoyl)phenyl]methyl}-1H-indole-6-carboxamide


Mass: 325.319 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H15N3O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#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 / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsThe sequence conflicts are due to Uniprot updating the reference sequence are the authors had ...The sequence conflicts are due to Uniprot updating the reference sequence are the authors had cloned their sequence.
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: 59.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL HDAC10, 2 mM inhibitor, 1:1000 trypsin:HDAC10, 0.168 M potassium phosphate monobasic, 0.032 M potassium phosphate dibasic, and 20% PEG3350 (v/v)

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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 PILATUS3 S 6M / Detector: PIXEL / Date: Aug 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.05→69.76 Å / Num. obs: 58990 / % possible obs: 100 % / Redundancy: 9 % / Biso Wilson estimate: 36.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.053 / Net I/σ(I): 12.12
Reflection shellResolution: 2.05→2.12 Å / Rmerge(I) obs: 1.349 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5813 / CC1/2: 0.685 / Rpim(I) all: 0.666

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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→69.76 Å / SU ML: 0.2726 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.4997
RfactorNum. reflection% reflection
Rfree0.2311 3062 5.19 %
Rwork0.1925 --
obs0.1945 58982 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.03 Å2
Refinement stepCycle: LAST / Resolution: 2.05→69.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4820 0 45 261 5126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00935064
X-RAY DIFFRACTIONf_angle_d0.98346915
X-RAY DIFFRACTIONf_chiral_restr0.1919789
X-RAY DIFFRACTIONf_plane_restr0.0066891
X-RAY DIFFRACTIONf_dihedral_angle_d22.53441801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.080.36031380.3182474X-RAY DIFFRACTION99.96
2.08-2.120.30861560.28622502X-RAY DIFFRACTION99.89
2.12-2.150.32971190.27092497X-RAY DIFFRACTION99.96
2.15-2.190.26471300.25692508X-RAY DIFFRACTION100
2.19-2.230.30481310.25482517X-RAY DIFFRACTION100
2.23-2.280.33111400.25642484X-RAY DIFFRACTION100
2.28-2.330.2831470.24092522X-RAY DIFFRACTION100
2.33-2.380.29271480.23332491X-RAY DIFFRACTION99.96
2.38-2.440.27091050.2312584X-RAY DIFFRACTION100
2.44-2.510.28781330.21362505X-RAY DIFFRACTION100
2.51-2.580.27441450.21962524X-RAY DIFFRACTION100
2.58-2.670.271230.21092518X-RAY DIFFRACTION100
2.67-2.760.27161510.21282506X-RAY DIFFRACTION100
2.76-2.870.26041400.20972554X-RAY DIFFRACTION100
2.87-30.24791520.20512522X-RAY DIFFRACTION99.96
3-3.160.22681150.20472553X-RAY DIFFRACTION100
3.16-3.360.2461450.19472563X-RAY DIFFRACTION100
3.36-3.620.21051360.18842563X-RAY DIFFRACTION99.96
3.62-3.980.19141530.1622550X-RAY DIFFRACTION100
3.98-4.560.1641350.14352602X-RAY DIFFRACTION100
4.56-5.740.17461510.15352635X-RAY DIFFRACTION99.93
5.74-69.760.22631690.17512746X-RAY DIFFRACTION99.59

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