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- PDB-9cbh: Crystal Structure of Danio rerio Histone Deacetylase 10 in Comple... -

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Basic information

Entry
Database: PDB / ID: 9cbh
TitleCrystal Structure of Danio rerio Histone Deacetylase 10 in Complex with p-Aminomethyl Phenylthioketone
ComponentsPolyamine deacetylase HDAC10
KeywordsHYDROLASE/INHIBITOR / Hydrolase / histone deacetylase / inhibitor / metallohydrolase / 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 / Polyamine deacetylase HDAC10
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGoulart Stollmaier, J. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM49758 United States
CitationJournal: Acs Med.Chem.Lett. / Year: 2024
Title: Design, Synthesis, and Structural Evaluation of Acetylated Phenylthioketone Inhibitors of HDAC10.
Authors: Goulart Stollmaier, J. / Watson, P.R. / Christianson, D.W.
History
DepositionJun 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

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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)75,5707
Polymers75,0561
Non-polymers5156
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.151, 80.151, 228.734
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac10 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: F1QCV2, acetylspermidine deacetylase, acetylputrescine deacetylase

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Non-polymers , 5 types, 13 molecules

#2: Chemical ChemComp-A1AVM / 1-[4-(aminomethyl)phenyl]-2-sulfanylethan-1-one


Mass: 181.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NOS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.83 Å3/Da / Density % sol: 56.47 % / Description: Diamond (rhombus) shaped
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL HDAC10 protein, 2 mM inhibitor, 0.18 M (NH4)3PO4, 0.1 M guanidine hydrochloride, 18% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2024
Details: Horizontal pre-focus bimorph mirror & KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→33.41 Å / Num. obs: 21853 / % possible obs: 99.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 73.32 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.076 / Net I/σ(I): 6.7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 9.2 % / Rmerge(I) obs: 2.075 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3144 / CC1/2: 0.523 / Rpim(I) all: 0.722 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
autoPROC1.0.5data reduction
Aimless0.7.13data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→33.41 Å / SU ML: 0.4363 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.8496
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2691 1994 9.15 %
Rwork0.2244 36758 -
obs0.2285 21782 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.85 Å2
Refinement stepCycle: LAST / Resolution: 2.8→33.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4490 0 25 7 4522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00254620
X-RAY DIFFRACTIONf_angle_d0.546329
X-RAY DIFFRACTIONf_chiral_restr0.0421744
X-RAY DIFFRACTIONf_plane_restr0.0047819
X-RAY DIFFRACTIONf_dihedral_angle_d12.32821530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.840.42871380.40311462X-RAY DIFFRACTION99.94
2.84-2.880.37921300.3871412X-RAY DIFFRACTION100
2.88-2.920.35511420.36581410X-RAY DIFFRACTION99.94
2.92-2.960.42181420.34171444X-RAY DIFFRACTION99.94
2.96-3.010.37171420.34611383X-RAY DIFFRACTION99.93
3.01-3.060.31081460.32481410X-RAY DIFFRACTION99.87
3.06-3.110.32191400.31541411X-RAY DIFFRACTION99.94
3.11-3.160.34891500.30671409X-RAY DIFFRACTION100
3.17-3.230.37611400.2991435X-RAY DIFFRACTION100
3.23-3.290.34491440.28281379X-RAY DIFFRACTION99.93
3.29-3.360.29471490.26871455X-RAY DIFFRACTION99.88
3.36-3.440.31621400.2641354X-RAY DIFFRACTION100
3.44-3.530.28831460.23231448X-RAY DIFFRACTION100
3.53-3.620.30731480.23191400X-RAY DIFFRACTION100
3.62-3.730.27331310.21581400X-RAY DIFFRACTION99.8
3.73-3.850.25171520.21981446X-RAY DIFFRACTION99.94
3.85-3.990.23071480.20561410X-RAY DIFFRACTION99.94
3.99-4.150.21661420.19361366X-RAY DIFFRACTION99.6
4.15-4.330.23631420.18771428X-RAY DIFFRACTION99.94
4.34-4.560.26131400.18171381X-RAY DIFFRACTION100
4.56-4.850.22841360.18921450X-RAY DIFFRACTION100
4.85-5.220.25941400.20071402X-RAY DIFFRACTION99.87
5.22-5.740.24121460.22041441X-RAY DIFFRACTION99.94
5.74-6.570.34071420.23571401X-RAY DIFFRACTION99.94
6.57-8.230.22521450.19241393X-RAY DIFFRACTION100
8.26-33.410.21491420.16741428X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.444847726830.1961644970690.249892072691.808848511790.470498348511.527747690640.01283018998240.1831993715550.1150462500890.219516172719-0.0314703934937-0.123131031348-0.0795858365238-0.04981032480320.03107472865310.6709358467960.2593224124490.04932603992580.5432664952690.02911330573470.81825023425712.776796835736.170454680532.244977336
22.170225520080.307004159361.097645024271.202636756650.4052222905982.3115627504-0.0648704365520.3406112537350.08047976991130.234589582826-0.007234514574730.1659433789630.0972773616625-0.3712804584540.09949238973280.6325022383830.1569987153110.1030959533450.844437409593-0.06086977071060.916940024241-5.9544625381319.561280543511.9597084954
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 338 )2 - 3381 - 337
22chain 'A' and (resid 339 through 676 )339 - 676338 - 624

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