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

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Basic information

Entry
Database: PDB / ID: 6gxa
TitleCrystal structure of Schistosoma mansoni HDAC8 complexed with an hydroxamate 2
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-TB8 / histone deacetylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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)204,39329
Polymers202,3324
Non-polymers2,06125
Water10,269570
1
A: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0707
Polymers50,5831
Non-polymers4876
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1638
Polymers50,5831
Non-polymers5807
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1638
Polymers50,5831
Non-polymers5807
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9976
Polymers50,5831
Non-polymers4145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.200, 70.441, 97.721
Angle α, β, γ (deg.)75.55, 78.23, 85.82
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, 595 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-TB8 / (~{E})-3-(2-chlorophenyl)-~{N}-oxidanyl-prop-2-enamide


Mass: 197.618 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H8ClNO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-DMF / DIMETHYLFORMAMIDE


Mass: 73.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H7NO
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 570 / 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: 2.26 Å3/Da / Density % sol: 45.66 %
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
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.1→45 Å / Num. obs: 88612 / % possible obs: 95.92 % / Redundancy: 2.9 % / Net I/σ(I): 7.83
Reflection shellResolution: 2.1→2.27 Å

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Processing

Software
NameVersionClassification
PHENIXdev_1702refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZ5

4bz5


Resolution: 2.1→43.146 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 24.27
RfactorNum. reflection% reflection
Rfree0.2259 10275 5.1 %
Rwork0.1747 --
obs0.1773 88602 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→43.146 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12999 0 24 570 13593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713511
X-RAY DIFFRACTIONf_angle_d0.99818368
X-RAY DIFFRACTIONf_dihedral_angle_d13.5294824
X-RAY DIFFRACTIONf_chiral_restr0.041970
X-RAY DIFFRACTIONf_plane_restr0.0052357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12390.3273300.27836435X-RAY DIFFRACTION96
2.1239-2.14890.30453440.26476287X-RAY DIFFRACTION97
2.1489-2.17510.30363690.25596306X-RAY DIFFRACTION97
2.1751-2.20260.28423460.24796394X-RAY DIFFRACTION97
2.2026-2.23160.33053590.2636223X-RAY DIFFRACTION96
2.2316-2.26220.31653270.25676353X-RAY DIFFRACTION96
2.2622-2.29450.31273240.25616340X-RAY DIFFRACTION97
2.2945-2.32870.2833340.22936370X-RAY DIFFRACTION97
2.3287-2.36510.26683610.22766293X-RAY DIFFRACTION97
2.3651-2.40390.25993330.21186429X-RAY DIFFRACTION97
2.4039-2.44530.27093700.20776403X-RAY DIFFRACTION97
2.4453-2.48980.27483040.22196364X-RAY DIFFRACTION98
2.4898-2.53770.29863760.21296348X-RAY DIFFRACTION97
2.5377-2.58950.2673680.20136417X-RAY DIFFRACTION97
2.5895-2.64580.26193910.19696307X-RAY DIFFRACTION98
2.6458-2.70730.27623280.18676433X-RAY DIFFRACTION98
2.7073-2.7750.24653760.18256311X-RAY DIFFRACTION97
2.775-2.850.22953020.17156465X-RAY DIFFRACTION98
2.85-2.93380.24623520.17186479X-RAY DIFFRACTION98
2.9338-3.02850.22592900.17076437X-RAY DIFFRACTION98
3.0285-3.13670.21173340.16866359X-RAY DIFFRACTION98
3.1367-3.26230.23143320.1666454X-RAY DIFFRACTION98
3.2623-3.41070.21543160.1626428X-RAY DIFFRACTION98
3.4107-3.59040.20523700.156363X-RAY DIFFRACTION97
3.5904-3.81520.18173250.14266402X-RAY DIFFRACTION97
3.8152-4.10960.18453520.13596306X-RAY DIFFRACTION97
4.1096-4.52280.1753020.12876420X-RAY DIFFRACTION97
4.5228-5.17630.16393220.13176388X-RAY DIFFRACTION97
5.1763-6.5180.19233800.1576406X-RAY DIFFRACTION98
6.518-43.15510.19623580.16256360X-RAY DIFFRACTION98
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)
10.99740.1009-0.02540.5236-0.26940.6572-0.0213-0.1399-0.10420.0711-0.0296-0.0806-0.01360.0341-0.00030.1229-0.0056-0.02310.16310.02280.130953.587124.943985.3022
20.9893-0.26750.0220.5533-0.0680.57710.037-0.1149-0.003-0.0053-0.0327-0.0173-0.0093-0.025400.1063-0.00210.00280.158-0.01020.131988.324942.9469.8944
30.4718-0.2265-0.00840.88610.10510.646-0.0359-0.01860.0039-0.04260.01920.047-0.03330.008300.1077-0.0043-0.00590.07350.00320.119444.74872.240340.4404
40.66170.093-0.1860.929-0.0870.6591-0.03220.0781-0.0283-0.149-0.0026-0.02120.0323-0.0081-00.1813-0.02010.00990.119-0.01560.111865.219735.695625.0121
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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