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- PDB-7p2s: Crystal structure of Schistosoma mansoni HDAC8 in complex with a ... -

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Basic information

Entry
Database: PDB / ID: 7p2s
TitleCrystal structure of Schistosoma mansoni HDAC8 in complex with a tricyclic thieno[3,2-b]indole capped hydroxamate-based inhibitor, chlorine derivative
ComponentsHistone deacetylase 8
KeywordsHYDROLASE / Inhibitor HISTONE DEACETYLASE (HDACi) / Complex Schistosoma mansoni HDAC8 + inhibitor / Active-site.
Function / homology
Function and homology information


histone deacetylase / histone deacetylase activity / heterochromatin formation / metal ion binding / nucleus
Similarity search - Function
: / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily
Similarity search - Domain/homology
Chem-4UI / : / histone deacetylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSaccoccia, F. / Gemma, S. / Campiani, G. / Ruberti, G.
Funding support Italy, 3items
OrganizationGrant numberCountry
Italian National Research Council (CNR) Italy
Ministero dell'Università e della Ricerca Italy
Regione Lazio (Italy) Italy
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 27, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4025
Polymers49,8341
Non-polymers5684
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-0 kcal/mol
Surface area16340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.832, 70.832, 179.968
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Histone deacetylase 8


Mass: 49834.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: HDAC8 / Production host: E. coli BL21(DE3) (bacteria) / References: UniProt: A5H660
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 424.511 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H17FN2O2S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
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: 2.26 Å3/Da / Density % sol: 45 %
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: Sep 18, 2019
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
ReflectionResolution: 2.2→48.25 Å / Num. obs: 24199 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.03 / Rrim(I) all: 0.107 / Net I/σ(I): 16.7 / Num. measured all: 307016 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.2712.81.972615720470.5840.5712.0531.4100
9.07-48.259.50.028416243610.0090.0360.999.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZ5

4bz5


Resolution: 2.2→48 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 14.434 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.263 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2405 1169 4.8 %RANDOM
Rwork0.2048 ---
obs0.2065 22956 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.76 Å2 / Biso mean: 54.011 Å2 / Biso min: 36.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å2-0 Å2
2--0.05 Å20 Å2
3----0.09 Å2
Refinement stepCycle: final / Resolution: 2.2→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3197 0 32 38 3267
Biso mean--75.54 46.71 -
Num. residues----399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0133322
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173027
X-RAY DIFFRACTIONr_angle_refined_deg1.1321.6384521
X-RAY DIFFRACTIONr_angle_other_deg1.1281.5746966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4245394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.48921.751177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33315514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6121519
X-RAY DIFFRACTIONr_chiral_restr0.0450.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023746
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02800
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 81 -
Rwork0.304 1643 -
all-1724 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -8.581 Å / Origin y: 21.726 Å / Origin z: 15.119 Å
111213212223313233
T0.1453 Å2-0.0081 Å20.0924 Å2-0.0128 Å2-0.0111 Å2--0.07 Å2
L1.4459 °20.0323 °2-0.9837 °2-2.3848 °20.3114 °2--2.2503 °2
S0.0121 Å °0.0108 Å °-0.1014 Å °-0.0215 Å °-0.0725 Å °0.056 Å °0.0164 Å °0.1039 Å °0.0604 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 435
2X-RAY DIFFRACTION1A501 - 504

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