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- PDB-6gxu: Crystal structure of Schistosoma mansoni HDAC8 complexed with an ... -

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Basic information

Entry
Database: PDB / ID: 6gxu
TitleCrystal structure of Schistosoma mansoni HDAC8 complexed with an hydroxamate 3
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 domain / Arginase; Chain A / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIMETHYLFORMAMIDE / Chem-FG8 / : / histone deacetylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.917 Å
AuthorsShaik, T.B. / Marek, M. / Romier, C.
Funding support France, 2items
OrganizationGrant numberCountry
European Commission241865 France
European Commission602080 France
CitationJournal: ChemMedChem / Year: 2018
Title: Synthesis, Crystallization Studies, and in vitro Characterization of Cinnamic Acid Derivatives as SmHDAC8 Inhibitors for the Treatment of Schistosomiasis.
Authors: Bayer, T. / Chakrabarti, A. / Lancelot, J. / Shaik, T.B. / Hausmann, K. / Melesina, J. / Schmidtkunz, K. / Marek, M. / Erdmann, F. / Schmidt, M. / Robaa, D. / Romier, C. / Pierce, R.J. / Jung, M. / Sippl, W.
History
DepositionJun 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)206,32549
Polymers202,3324
Non-polymers3,99345
Water9,728540
1
A: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,49011
Polymers50,5831
Non-polymers90710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,63613
Polymers50,5831
Non-polymers1,05312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,78215
Polymers50,5831
Non-polymers1,19914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,41710
Polymers50,5831
Non-polymers8349
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.420, 70.460, 97.910
Angle α, β, γ (deg.)77.96, 75.94, 85.97
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, histone deacetylase

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Non-polymers , 6 types, 585 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-FG8 / (~{E})-3-[2-(4-chlorophenyl)sulfanylphenyl]-~{N}-oxidanyl-prop-2-enamide


Mass: 305.779 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H12ClNO2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical...
ChemComp-DMF / DIMETHYLFORMAMIDE


Mass: 73.094 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C3H7NO
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NA,K L-TARTRATE, 21% (W/V) PEG3350

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Data collection

DiffractionMean temperature: 100 K
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: 1.917→46.55 Å / Num. obs: 118789 / % possible obs: 86.69 % / Redundancy: 1.8 % / Net I/σ(I): 5.58
Reflection shellResolution: 1.917→1.986 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZ5

4bz5


Resolution: 1.917→46.549 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 27.77
RfactorNum. reflection% reflection
Rfree0.2484 5940 5 %
Rwork0.2012 --
obs0.2036 118753 86.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.917→46.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12850 0 241 540 13631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713456
X-RAY DIFFRACTIONf_angle_d0.88218263
X-RAY DIFFRACTIONf_dihedral_angle_d14.4147850
X-RAY DIFFRACTIONf_chiral_restr0.0511949
X-RAY DIFFRACTIONf_plane_restr0.0062410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9169-1.93870.391090.32342062X-RAY DIFFRACTION48
1.9387-1.96150.36872100.31174002X-RAY DIFFRACTION91
1.9615-1.98540.31832040.283859X-RAY DIFFRACTION91
1.9854-2.01050.31752090.27043981X-RAY DIFFRACTION90
2.0105-2.0370.33652020.26293843X-RAY DIFFRACTION89
2.037-2.06490.31032020.25443825X-RAY DIFFRACTION88
2.0649-2.09440.28441990.24653770X-RAY DIFFRACTION87
2.0944-2.12570.32691980.24483780X-RAY DIFFRACTION87
2.1257-2.15890.31042060.24043915X-RAY DIFFRACTION91
2.1589-2.19430.27782060.22413914X-RAY DIFFRACTION90
2.1943-2.23210.28992000.22253789X-RAY DIFFRACTION89
2.2321-2.27270.30841990.22973781X-RAY DIFFRACTION86
2.2727-2.31640.28921990.22673775X-RAY DIFFRACTION88
2.3164-2.36370.27431990.21993793X-RAY DIFFRACTION87
2.3637-2.41510.29412000.21553785X-RAY DIFFRACTION87
2.4151-2.47120.25991980.20963765X-RAY DIFFRACTION87
2.4712-2.5330.25362030.21243847X-RAY DIFFRACTION88
2.533-2.60150.26061980.20443780X-RAY DIFFRACTION87
2.6015-2.67810.24041980.21253752X-RAY DIFFRACTION87
2.6781-2.76450.28521970.2043747X-RAY DIFFRACTION86
2.7645-2.86330.26092040.20033864X-RAY DIFFRACTION89
2.8633-2.97790.26562020.20043841X-RAY DIFFRACTION89
2.9779-3.11340.242060.19553923X-RAY DIFFRACTION90
3.1134-3.27750.24312030.18493859X-RAY DIFFRACTION89
3.2775-3.48280.21782000.17313785X-RAY DIFFRACTION87
3.4828-3.75160.21541920.17463644X-RAY DIFFRACTION84
3.7516-4.12890.20641950.16913709X-RAY DIFFRACTION85
4.1289-4.72590.20251980.16863762X-RAY DIFFRACTION87
4.7259-5.95220.22081990.18563791X-RAY DIFFRACTION87
5.9522-46.56270.22182050.20593870X-RAY DIFFRACTION89
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)
10.62360.0898-0.12680.6179-0.31010.48920.0455-0.0399-0.02850.0618-0.0576-0.02860.0020.0423-0.00070.1553-0.0258-0.00640.1884-0.00280.150453.839225.49885.9853
20.7102-0.2764-0.00880.4364-0.00730.47340.01980.00040.0415-0.0011-0.0363-0.019-0.05190.007700.10520.0023-0.01010.1244-0.00080.121388.507143.107170.3093
30.4006-0.1127-0.08440.92460.15280.5119-0.03770.002-0.0053-0.03090.03810.0405-0.0026-0.038800.11490.0101-0.00870.08310.00550.092644.86912.256441.1726
40.50950.1269-0.22570.8147-0.07690.461-0.03540.0157-0.0425-0.06180.0058-0.01120.0015-0.0121-0.00030.1774-0.01270.00590.1467-0.00540.155465.102335.966325.4126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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