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- PDB-7poz: Crystal structure of Schistosoma mansoni HDAC8 with DMSO bound in... -

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Basic information

Entry
Database: PDB / ID: 7poz
TitleCrystal structure of Schistosoma mansoni HDAC8 with DMSO bound in the active site
ComponentsHistone deacetylase 8
KeywordsHYDROLASE / SmHDAC8 / histone-deacetilase / double-conformation
Function / homology
Function and homology information


histone deacetylase activity, hydrolytic mechanism / histone deacetylase / 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
: / histone deacetylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSaccoccia, F. / Ruberti, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionSep 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 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

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Assembly

Deposited unit
A: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1486
Polymers49,8341
Non-polymers3145
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-37 kcal/mol
Surface area16600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.738, 70.738, 179.462
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#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: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5H660

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Non-polymers , 5 types, 190 molecules

#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 21% PEG3350, 200mM Na/K-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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→43.73 Å / Num. obs: 34801 / % possible obs: 95.8 % / Redundancy: 4.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.049 / Rrim(I) all: 0.108 / Net I/σ(I): 9.8
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
1.9-1.944.40.947981922410.6030.4961.0741.497.9
9.11-43.693.80.03813313500.9980.0210.04328.689.2

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bz5

4bz5


Resolution: 1.9→43.73 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 6.934 / SU ML: 0.098 / SU R Cruickshank DPI: 0.1427 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1714 4.9 %RANDOM
Rwork0.1697 ---
obs0.1719 33072 94.34 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 145.55 Å2 / Biso mean: 31.397 Å2 / Biso min: 14.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å2-0 Å2
2---0.8 Å2-0 Å2
3---1.6 Å2
Refinement stepCycle: final / Resolution: 1.9→43.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3244 0 13 185 3442
Biso mean--31.14 36.63 -
Num. residues----405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133394
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173131
X-RAY DIFFRACTIONr_angle_refined_deg1.2571.6344618
X-RAY DIFFRACTIONr_angle_other_deg1.2491.5757216
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9175412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9421.91178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60915541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3781519
X-RAY DIFFRACTIONr_chiral_restr0.0590.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023823
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02811
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 113 -
Rwork0.247 2469 -
all-2582 -
obs--96.85 %
Refinement TLS params.Method: refined / Origin x: -8.3511 Å / Origin y: 21.7802 Å / Origin z: 15.157 Å
111213212223313233
T0.051 Å2-0.0112 Å20.0432 Å2-0.0111 Å2-0.0034 Å2--0.0417 Å2
L0.1373 °2-0.0161 °2-0.1556 °2-0.4062 °20.0102 °2--0.2889 °2
S-0.0255 Å °0.0008 Å °-0.0264 Å °0.004 Å °-0.0066 Å °0.019 Å °0.0061 Å °0.0338 Å °0.0321 Å °

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