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

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Basic information

Entry
Database: PDB / ID: 9cbi
TitleCrystal Structure of Danio rerio Histone Deacetylase 10 in Complex with p-Aminoethyl 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: 2.5 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)75,83311
Polymers75,0561
Non-polymers77710
Water46826
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.728, 80.728, 240.440
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 , 6 types, 36 molecules

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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-A1AVQ / 1-[4-(2-aminoethyl)phenyl]-2-sulfanylethan-1-one


Mass: 195.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13NOS / Feature type: SUBJECT OF INVESTIGATION
#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: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.01 Å3/Da / Density % sol: 59.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL HDAC10 protein, 2 mM inhibitor, 0.2 M KH2PO4, 20% (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: 2.5→34.59 Å / Num. obs: 32444 / % possible obs: 100 % / Redundancy: 9.8 % / Biso Wilson estimate: 68.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.044 / Net I/σ(I): 9.1
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 10.4 % / Rmerge(I) obs: 2.001 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3629 / CC1/2: 0.582 / Rpim(I) all: 0.647 / % 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: 2.5→34.59 Å / SU ML: 0.3469 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.4829
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2319 2009 6.23 %
Rwork0.2146 56826 -
obs0.2157 32367 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.68 Å2
Refinement stepCycle: LAST / Resolution: 2.5→34.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4439 0 42 26 4507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224581
X-RAY DIFFRACTIONf_angle_d0.54316254
X-RAY DIFFRACTIONf_chiral_restr0.0416727
X-RAY DIFFRACTIONf_plane_restr0.0045810
X-RAY DIFFRACTIONf_dihedral_angle_d12.58921536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.42881390.39692168X-RAY DIFFRACTION99.83
2.53-2.560.37111420.39292033X-RAY DIFFRACTION99.77
2.56-2.60.3681440.37292167X-RAY DIFFRACTION99.78
2.6-2.640.39771440.3612080X-RAY DIFFRACTION99.91
2.64-2.680.42811400.35082085X-RAY DIFFRACTION100
2.68-2.720.36271380.31062057X-RAY DIFFRACTION99.73
2.72-2.760.38821420.32662101X-RAY DIFFRACTION99.87
2.76-2.810.33971380.29912144X-RAY DIFFRACTION100
2.81-2.860.33371440.28562122X-RAY DIFFRACTION100
2.86-2.920.28271340.2842072X-RAY DIFFRACTION100
2.92-2.980.27011450.2742142X-RAY DIFFRACTION100
2.98-3.040.32051300.27252083X-RAY DIFFRACTION100
3.04-3.110.26161410.25762142X-RAY DIFFRACTION99.91
3.11-3.190.28321260.25592072X-RAY DIFFRACTION99.95
3.19-3.280.27981380.25042092X-RAY DIFFRACTION99.96
3.28-3.370.24851460.23942140X-RAY DIFFRACTION100
3.37-3.480.23381420.2232096X-RAY DIFFRACTION100
3.48-3.60.24931400.20532074X-RAY DIFFRACTION100
3.6-3.750.20061360.19532119X-RAY DIFFRACTION99.96
3.75-3.920.22111390.19762096X-RAY DIFFRACTION99.96
3.92-4.130.18731460.18982100X-RAY DIFFRACTION99.82
4.13-4.380.21391340.16992118X-RAY DIFFRACTION100
4.38-4.720.16241430.16922125X-RAY DIFFRACTION99.78
4.72-5.190.18551340.18022106X-RAY DIFFRACTION100
5.2-5.940.25781460.21462079X-RAY DIFFRACTION99.87
5.95-7.470.20371400.20372111X-RAY DIFFRACTION99.91
7.48-34.590.19611450.17392102X-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)
11.687714180980.0585201798393-0.07996978909061.952179718020.5340482814331.581410403230.01911066234880.2416734060750.05349994966440.151183736441-0.08052650823730.01296390165-0.00154721797217-0.05978572968770.07011220177250.6712183426870.2403727078560.1141662162750.5711258249990.08235687141030.73020660582612.456290030337.474693700133.4830243661
21.676691055940.7684130389171.664053041140.69372097765-0.1660778042894.177870658850.01780932591010.481478092380.000780641684672-0.0547577963522-0.1008091418680.2382033854690.113402155091-0.6422598512620.1306604581340.6179122642620.2194405641820.08610626126581.28222956775-0.07743065173211.07560946951-13.964998025928.12187570665.02959640633
32.432235465430.3160242149251.847613597143.10315216654-1.707474918852.75316652540.3767211499120.338850555334-0.285470468577-0.247214835126-0.2922079410990.292620874160.699470197948-0.1956143861680.03326638553020.8499683009190.1745959858670.02497793744731.00641414568-0.177744434581.02339187231-4.1788824972314.93425104769.72836430156
42.251127723780.2727463622281.58540057722.93024723046-1.434809458512.65478837059-0.000758013440267-0.0892339580802-0.07500225063320.351303896997-0.1677575404950.1293443654620.264428615489-0.1281879289720.1611823901880.7306571836230.1635639716290.1455473828460.769260910347-0.110808091110.828865531491-2.9382704479720.023628662915.846964887
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 1 through 354 )1 - 3541 - 354
22chain 'A' and (resid 355 through 503 )355 - 503355 - 449
33chain 'A' and (resid 504 through 567 )504 - 567450 - 511
44chain 'A' and (resid 568 through 676 )568 - 676512 - 613

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