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- PDB-7p3s: Crystal structure of Schistosoma mansoni HDAC8 complexed with a b... -

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Basic information

Entry
Database: PDB / ID: 7p3s
TitleCrystal structure of Schistosoma mansoni HDAC8 complexed with a benzohydroxamate inhibitor 12
ComponentsHistone deacetylase
KeywordsHYDROLASE / Epigenetics / Histone deacetylase / HDAC8 / Selective inhibitor / Pathogen
Function / homology
Function and homology information


histone deacetylase / histone deacetylase activity / negative regulation of transcription by RNA polymerase II / nucleus / 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
Chem-5IB / : / histone deacetylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.546 Å
AuthorsShaik, T.B. / Romier, C.
Funding supportEuropean Union, 2items
OrganizationGrant numberCountry
European Communitys Seventh Framework Programme241865European Union
European Communitys Seventh Framework Programme602080European Union
CitationJournal: Eur.J.Med.Chem. / Year: 2021
Title: Synthesis, structure-activity relationships, cocrystallization and cellular characterization of novel smHDAC8 inhibitors for the treatment of schistosomiasis.
Authors: Ghazy, E. / Heimburg, T. / Lancelot, J. / Zeyen, P. / Schmidtkunz, K. / Truhn, A. / Darwish, S. / Simoben, C.V. / Shaik, T.B. / Erdmann, F. / Schmidt, M. / Robaa, D. / Romier, C. / Jung, M. ...Authors: Ghazy, E. / Heimburg, T. / Lancelot, J. / Zeyen, P. / Schmidtkunz, K. / Truhn, A. / Darwish, S. / Simoben, C.V. / Shaik, T.B. / Erdmann, F. / Schmidt, M. / Robaa, D. / Romier, C. / Jung, M. / Pierce, R. / Sippl, W.
History
DepositionJul 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)205,14928
Polymers202,3324
Non-polymers2,81724
Water20,2491124
1
A: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3798
Polymers50,5831
Non-polymers7967
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1956
Polymers50,5831
Non-polymers6125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2877
Polymers50,5831
Non-polymers7046
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2877
Polymers50,5831
Non-polymers7046
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.390, 70.390, 97.940
Angle α, β, γ (deg.)78.050, 75.570, 85.690
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Histone deacetylase


Mass: 50583.027 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 (E. coli) / References: UniProt: A5H660

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Non-polymers , 5 types, 1148 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.: 8 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-5IB / ~{N}-[2-methoxy-5-(oxidanylcarbamoyl)phenyl]dibenzofuran-4-carboxamide


Mass: 376.362 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H16N2O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1124 / 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: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M NA,K L-TARTRATE, 21% (W/V) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.006365 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006365 Å / Relative weight: 1
ReflectionResolution: 1.546→46.52 Å / Num. obs: 235033 / % possible obs: 90.2 % / Redundancy: 1.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.057 / Net I/σ(I): 7.74
Reflection shellResolution: 1.546→1.64 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 1.35 / Num. unique obs: 37886 / CC1/2: 0.575 / % possible all: 89.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZ5

4bz5


Resolution: 1.546→46.515 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 19.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1934 11750 5 %
Rwork0.169 223256 -
obs0.1703 235006 90.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.21 Å2 / Biso mean: 24.9727 Å2 / Biso min: 8.94 Å2
Refinement stepCycle: final / Resolution: 1.546→46.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12945 0 172 1124 14241
Biso mean--55.82 32.77 -
Num. residues----1620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613666
X-RAY DIFFRACTIONf_angle_d0.84918645
X-RAY DIFFRACTIONf_chiral_restr0.0532006
X-RAY DIFFRACTIONf_plane_restr0.0062488
X-RAY DIFFRACTIONf_dihedral_angle_d11.6858117
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5461-1.56370.29293670.2791698084
1.5637-1.58210.27933910.2628741991
1.5821-1.60140.27424030.2577766592
1.6014-1.62170.28063940.2465748391
1.6217-1.6430.27923980.2389755191
1.643-1.66550.24553950.2275751091
1.6655-1.68930.23253960.2078753491
1.6893-1.71450.2424030.2107765192
1.7145-1.74130.23613900.2033740491
1.7413-1.76990.24093930.2023747090
1.7699-1.80040.24493880.1969738290
1.8004-1.83310.23313820.194725588
1.8331-1.86840.20963830.1832727488
1.8684-1.90650.20364080.181774993
1.9065-1.9480.21073980.1701755992
1.948-1.99330.19474030.162766693
1.9933-2.04320.19764030.1568765893
2.0432-2.09840.18613950.1624750091
2.0984-2.16010.18184030.1604764693
2.1601-2.22990.17523980.1548756091
2.2299-2.30960.18733840.1587730189
2.3096-2.4020.19033900.1595740689
2.402-2.51130.17943850.1627731788
2.5113-2.64370.20043650.1667694585
2.6437-2.80940.19423930.1617747790
2.8094-3.02620.19713860.1607733589
3.0262-3.33070.1933860.1625734489
3.3307-3.81250.14953900.1509739490
3.8125-4.80250.16093810.1386723988
4.8025-46.5150.18073990.1681758292
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)
10.70410.0619-0.24010.4984-0.27220.62-0.0004-0.0806-0.0270.054-0.0292-0.044-0.00560.0567-0.00220.0589-0.0126-0.02060.10430.00380.070553.918125.185.4754
20.5915-0.1840.16670.3209-0.060.5192-0.0053-0.01810.02560.0002-0.0177-0.0047-0.0216-0.01010.00060.09060.0012-0.00070.1208-0.00050.122288.356242.759670.0777
30.3151-0.1381-0.09020.81730.20620.5403-0.0137-0.01010.0029-0.07440.0083-0.0036-0.0195-0.04410.00340.12090.0036-0.00190.08320.00610.09344.59552.625540.692
40.5490.0609-0.28780.6046-0.06550.6436-0.03460.067-0.0774-0.0215-0.0051-0.02840.01550.01590.00020.1416-0.01270.01450.1114-0.01520.133765.026135.757826.0509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA2 - 802
2X-RAY DIFFRACTION2chain BB2 - 800
3X-RAY DIFFRACTION3chain CC2 - 801
4X-RAY DIFFRACTION4chain DD2 - 801

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