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

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Basic information

Entry
Database: PDB / ID: 9cbf
TitleCrystal Structure of Danio rerio Histone Deacetylase 10 in Complex with m-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: 2.26 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)75,75710
Polymers75,0561
Non-polymers7019
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.411, 80.411, 236.953
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, 23 molecules

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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-A1AVR / 1-[3-(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
#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.: 14 / 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: 2.95 Å3/Da / Density % sol: 58.25 % / Description: Diamond (rhombus) shaped
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: 2.26→34.35 Å / Num. obs: 39402 / % possible obs: 91.7 % / Redundancy: 9.3 % / Biso Wilson estimate: 56.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.043 / Net I/σ(I): 9.1
Reflection shellResolution: 2.26→2.33 Å / Redundancy: 10 % / Rmerge(I) obs: 2.33 / Mean I/σ(I) obs: 1 / Num. unique obs: 3873 / CC1/2: 0.539 / Rpim(I) all: 0.77 / % 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: 2.26→34.35 Å / SU ML: 0.3698 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.6815
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2584 1986 5.08 %
Rwork0.2351 70177 -
obs0.2363 39303 91.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.81 Å2
Refinement stepCycle: LAST / Resolution: 2.26→34.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4409 0 37 14 4460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00194533
X-RAY DIFFRACTIONf_angle_d0.4816188
X-RAY DIFFRACTIONf_chiral_restr0.0402724
X-RAY DIFFRACTIONf_plane_restr0.0039797
X-RAY DIFFRACTIONf_dihedral_angle_d11.47461512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.280.45631590.45442839X-RAY DIFFRACTION99.83
2.28-2.310.48171480.43982828X-RAY DIFFRACTION99.93
2.31-2.350.43931550.42592797X-RAY DIFFRACTION99.93
2.35-2.380.36521480.3992839X-RAY DIFFRACTION99.83
2.38-2.410.37811500.39532861X-RAY DIFFRACTION99.97
2.41-2.450.35921480.3762830X-RAY DIFFRACTION99.87
2.45-2.490.36061540.34692830X-RAY DIFFRACTION99.87
2.49-2.540.33371500.31942848X-RAY DIFFRACTION100
2.54-2.580.35981540.33122869X-RAY DIFFRACTION99.97
2.58-2.610.4602760.38821567X-RAY DIFFRACTION94.97
2.71-2.740.2843800.29911533X-RAY DIFFRACTION99.75
2.74-2.810.28691580.29452883X-RAY DIFFRACTION99.93
2.81-2.880.25161580.28512865X-RAY DIFFRACTION99.87
2.88-2.950.26771450.27542814X-RAY DIFFRACTION99.9
2.95-3.040.2781520.2782806X-RAY DIFFRACTION99.93
3.04-3.140.26211520.26792813X-RAY DIFFRACTION99.9
3.14-3.250.28821620.25392859X-RAY DIFFRACTION99.97
3.25-3.380.27021520.24432856X-RAY DIFFRACTION100
3.38-3.540.30461440.24642852X-RAY DIFFRACTION99.87
3.54-3.720.25641020.24141750X-RAY DIFFRACTION62.86
3.72-3.950.26931500.2082841X-RAY DIFFRACTION99.87
3.96-4.260.22291640.18382851X-RAY DIFFRACTION99.9
4.26-4.690.20721480.18382835X-RAY DIFFRACTION99.77
4.69-5.360.20281500.19342858X-RAY DIFFRACTION99.87
5.36-6.740.27041420.22462829X-RAY DIFFRACTION99.87
6.75-34.350.19471530.17872824X-RAY DIFFRACTION99.73
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)
11.600401158160.2217031511050.3598923457471.064492461350.4387822826491.200555428030.0867992595404-0.1501329175550.0267527245946-0.106620963068-0.100205408883-0.0831463560635-0.0425263366996-0.01934066883850.01223582659360.768227804005-0.1809638770010.09331179008030.415530823631-0.02999045520440.76399265885238.64247039478.0496303442-6.29805374492
20.896645549346-1.145034756960.6898641893281.52416825045-1.358868249513.006085179480.2011861004370.0515520618810.0264325469755-0.442625674184-0.2340588176190.00783106003162-0.291740007979-0.3354314701380.02851445058720.917837227733-0.004755696377610.003540475157320.464122522924-0.1205891467050.86023393074417.278100085718.8483555256-28.4728634937
31.69256920665-0.2621326452120.8960056725561.74393019002-2.576753733144.139366252580.3578893146910.1945813817760.485608837599-0.894778284994-0.2507930313560.3696678967560.146471980647-0.212366441192-0.09172625075881.150337691550.109299430337-0.01143115811510.552807728022-0.09660464991590.97533028517714.552957229219.1969318123-37.1561903259
47.71591031162-3.2400047918-0.1262078662614.45978482274-3.634232761384.86661787986-0.0612686006533-0.370857560319-0.0636574500799-0.3857115589750.1590210259480.5930921848260.239916552196-0.566289978151-0.06057407439480.773772688989-0.11487199867-0.00549790394610.516891177957-0.1433596873770.82377478492811.214585579711.0770827257-25.7516857703
50.737130826441-0.0853619029142-0.01612970346920.320550782487-0.8391616713232.250661930380.0842663844651-0.3870156908330.2731784105750.210347661535-0.2612279742550.402883551974-0.305205662722-0.2634582964180.1455930877350.9720507365660.01909274540920.05107328976740.56312645742-0.2264931139621.099622171816.290895889422.6319049746-21.8920487785
65.03348795950.159600676888-1.129842085290.491991210601-1.170639719994.365157959320.0687713486117-0.2546127572030.102817606711-0.06439147152310.09581983504260.2548390486050.606868182547-0.33085313859-0.1604511552420.91172015355-0.1858680925790.0261900610670.516552020737-0.1146048653341.0128057175612.5655506437-3.69482836349-23.5907392156
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 338 )1 - 3381 - 338
22chain 'A' and (resid 339 through 476 )339 - 476339 - 421
33chain 'A' and (resid 477 through 528 )477 - 528422 - 473
44chain 'A' and (resid 529 through 597 )529 - 597474 - 534
55chain 'A' and (resid 598 through 647 )598 - 647535 - 580
66chain 'A' and (resid 648 through 676 )648 - 676581 - 609

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