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- PDB-7p2t: Tetartohedrally twinned crystal structure of Schistosoma mansoni ... -

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Basic information

Entry
Database: PDB / ID: 7p2t
TitleTetartohedrally twinned crystal structure of Schistosoma mansoni HDAC8 in complex with a tricyclic thieno[3,2-b]indole capped hydroxamate-based inhibitor, bromine derivative
ComponentsHistone deacetylase 8
KeywordsHYDROLASE / SmHDAC8 / active-site / HDACi / histone-deacetilase inhibitor complex / tetartohedral / twinning
Function / homology
Function and homology information


histone deacetylase / chromatin organization / metal ion binding
Similarity search - Function
Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily
Similarity search - Domain/homology
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / Chem-4VX / : / histone deacetylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSaccoccia, F. / Gemma, S. / Campiani, G. / Ruberti, G.
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Crystal structures of Schistosoma mansoni histone deacetylase 8 reveal a novel binding site for allosteric inhibitors.
Authors: Saccoccia, F. / Pozzetti, L. / Gimmelli, R. / Butini, S. / Guidi, A. / Papoff, G. / Giannaccari, M. / Brogi, S. / Scognamiglio, V. / Gemma, S. / Ruberti, G. / Campiani, G.
History
DepositionJul 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 28, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone deacetylase 8
B: Histone deacetylase 8
C: Histone deacetylase 8
D: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,21125
Polymers199,3374
Non-polymers2,87421
Water1,11762
1
A: Histone deacetylase 8
hetero molecules


  • defined by author&software
  • Evidence: Steady-state kinetics experiments confirmed that ligand behaved as a competitive inhibitor; fluorescence spectra - at equilibrium - confirmed the binding in the active site; all of the ...Evidence: Steady-state kinetics experiments confirmed that ligand behaved as a competitive inhibitor; fluorescence spectra - at equilibrium - confirmed the binding in the active site; all of the above experiments were confirmed by dedicated mutant form. More details will be released in related publication
  • 50.5 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)50,4635
Polymers49,8341
Non-polymers6294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5026
Polymers49,8341
Non-polymers6685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6247
Polymers49,8341
Non-polymers7906
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6217
Polymers49,8341
Non-polymers7876
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.205, 99.003, 178.585
Angle α, β, γ (deg.)90.000, 91.300, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Histone deacetylase 8 /


Mass: 49834.219 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: HDAC8 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5H660

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Non-polymers , 6 types, 83 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-4VX / 5-[[(2R)-7-bromanyl-2-phenyl-2,3-dihydrothieno[3,2-b]indol-4-yl]methyl]-N-oxidanyl-thiophene-2-carboxamide


Mass: 485.417 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H17BrN2O2S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 20-22% PEG 3350, 200mM sodium/potassium tartrate / Temp details: cold room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2020
RadiationMonochromator: Double Crystal Si111 with LN2 closed loop cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.48
11-K, -H, -L20.189
11K, H, -L30.171
11h,-k,-l40.16
ReflectionResolution: 2.3→178.539 Å / Num. all: 76754 / Num. obs: 76754 / % possible obs: 100 % / Redundancy: 6.5 % / Rpim(I) all: 0.087 / Rrim(I) all: 0.226 / Rsym value: 0.208 / Net I/av σ(I): 2.3 / Net I/σ(I): 4.6 / Num. measured all: 501220
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.3-2.426.21.3460.669613111620.5831.471.3461.2100
2.42-2.576.40.9790.867881105580.4161.0660.9791.7100
2.57-2.756.60.6571.26596099340.2740.7130.6572.5100
2.75-2.976.50.4581.65971192370.1940.4980.4583.4100
2.97-3.256.60.332.25630885170.1380.3580.334.9100
3.25-3.646.80.2412.65291277310.0980.260.2416.8100
3.64-4.26.60.1813.44521268180.0750.1960.1818.2100
4.2-5.146.70.163.93854157830.0660.1740.169.2100
5.14-7.276.50.1553.82933545000.0650.1680.1558.6100
7.27-48.0636.30.095.21574725140.0380.0980.099.699.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bz5

4bz5


Resolution: 2.3→48.063 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.294 --RANDOM
obs0.2794 73098 100 %-
Displacement parametersBiso max: 119.88 Å2 / Biso mean: 50.183 Å2 / Biso min: 20.72 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12722 0 147 62 12931

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