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- PDB-6hsh: Crystal structure of Schistosoma mansoni HDAC8 complexed with Qui... -

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Basic information

Entry
Database: PDB / ID: 6hsh
TitleCrystal structure of Schistosoma mansoni HDAC8 complexed with Quisinostat
ComponentsHistone deacetylase
KeywordsHYDROLASE / Epigenetics / Histone deacetylase / HDAC8 / Selective inhibitor / Pathogen
Function / homology
Function and homology information


histone deacetylase / histone deacetylase activity / heterochromatin formation / metal ion binding / nucleus
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-GOK / : / histone deacetylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.545 Å
AuthorsShaik, T.B. / Marek, M. / Romier, C.
Funding support France, 2items
OrganizationGrant numberCountry
European Commission241865 France
European Commission602080 France
CitationJournal: J. Med. Chem. / Year: 2018
Title: Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants.
Authors: Marek, M. / Shaik, T.B. / Heimburg, T. / Chakrabarti, A. / Lancelot, J. / Ramos-Morales, E. / Da Veiga, C. / Kalinin, D. / Melesina, J. / Robaa, D. / Schmidtkunz, K. / Suzuki, T. / Holl, R. ...Authors: Marek, M. / Shaik, T.B. / Heimburg, T. / Chakrabarti, A. / Lancelot, J. / Ramos-Morales, E. / Da Veiga, C. / Kalinin, D. / Melesina, J. / Robaa, D. / Schmidtkunz, K. / Suzuki, T. / Holl, R. / Ennifar, E. / Pierce, R.J. / Jung, M. / Sippl, W. / Romier, C.
History
DepositionOct 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.3Jan 24, 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 / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.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)207,98457
Polymers202,3324
Non-polymers5,65253
Water19,8531102
1
A: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,65212
Polymers50,5831
Non-polymers1,06911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,13814
Polymers50,5831
Non-polymers1,55513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,45018
Polymers50,5831
Non-polymers1,86717
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,74413
Polymers50,5831
Non-polymers1,16112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.750, 70.800, 97.820
Angle α, β, γ (deg.)78.03, 75.67, 85.74
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, 1155 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-GOK / 2-[4-[[(1-methylindol-3-yl)methylamino]methyl]piperidin-1-yl]-~{N}-oxidanyl-pyrimidine-5-carboxamide


Mass: 394.470 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H26N6O2
#5: Chemical...
ChemComp-DMF / DIMETHYLFORMAMIDE


Mass: 73.094 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C3H7NO
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1102 / 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: 2.29 Å3/Da / Density % sol: 46.4 %
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: ESRF / Beamline: ID29 / Wavelength: 1.072522 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072522 Å / Relative weight: 1
ReflectionResolution: 1.545→46.47 Å / Num. obs: 218343 / % possible obs: 82.81 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.05004 / Net I/σ(I): 8.31
Reflection shellResolution: 1.545→1.6 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.6931 / Mean I/σ(I) obs: 0.95 / Num. unique obs: 11192 / % possible all: 42.36

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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: 1.545→46.47 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 23.7
RfactorNum. reflection% reflection
Rfree0.2019 10917 5 %
Rwork0.1684 --
obs0.1701 218321 82.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.545→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13059 0 369 1102 14530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713846
X-RAY DIFFRACTIONf_angle_d0.89118805
X-RAY DIFFRACTIONf_dihedral_angle_d13.4998148
X-RAY DIFFRACTIONf_chiral_restr0.0551998
X-RAY DIFFRACTIONf_plane_restr0.0062531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.545-1.56250.36651450.36442762X-RAY DIFFRACTION33
1.5625-1.58090.37211950.35493707X-RAY DIFFRACTION44
1.5809-1.60020.36152170.36014120X-RAY DIFFRACTION49
1.6002-1.62040.35822420.34774603X-RAY DIFFRACTION55
1.6204-1.64180.36442770.33435263X-RAY DIFFRACTION63
1.6418-1.66430.35343110.32485913X-RAY DIFFRACTION71
1.6643-1.6880.34233860.31657321X-RAY DIFFRACTION87
1.688-1.71320.32953880.30677373X-RAY DIFFRACTION89
1.7132-1.740.32993940.2847484X-RAY DIFFRACTION90
1.74-1.76850.2823980.25897556X-RAY DIFFRACTION90
1.7685-1.7990.29133860.23447347X-RAY DIFFRACTION89
1.799-1.83170.24243880.22137362X-RAY DIFFRACTION88
1.8317-1.8670.2463880.21387375X-RAY DIFFRACTION88
1.867-1.90510.23913730.20997087X-RAY DIFFRACTION85
1.9051-1.94650.2343950.20277497X-RAY DIFFRACTION90
1.9465-1.99180.22674000.19367606X-RAY DIFFRACTION90
1.9918-2.04160.21794000.16927599X-RAY DIFFRACTION91
2.0416-2.09680.19283960.16077519X-RAY DIFFRACTION91
2.0968-2.15850.19233990.15857584X-RAY DIFFRACTION91
2.1585-2.22820.18753920.15127461X-RAY DIFFRACTION90
2.2282-2.30780.19433890.15757381X-RAY DIFFRACTION88
2.3078-2.40020.19774040.15517669X-RAY DIFFRACTION91
2.4002-2.50940.19994040.15577694X-RAY DIFFRACTION92
2.5094-2.64170.20014060.16017707X-RAY DIFFRACTION93
2.6417-2.80720.18214060.15357714X-RAY DIFFRACTION92
2.8072-3.02390.19444010.15047618X-RAY DIFFRACTION91
3.0239-3.32820.18024130.14947848X-RAY DIFFRACTION94
3.3282-3.80960.16864100.13747794X-RAY DIFFRACTION93
3.8096-4.79890.15514100.12517777X-RAY DIFFRACTION93
4.7989-46.49360.18974040.16117663X-RAY DIFFRACTION92
Refinement TLS params.

S33: -0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.68550.1732-0.19990.4201-0.29560.56030.007-0.0836-0.01940.034-0.0206-0.01640.00080.02820.13-0.0034-0.0090.1721-0.00180.139653.80224.522686.1176
20.6155-0.23060.0650.3994-0.13610.4095-0.009-0.02060.048-0.0043-0.0102-0.0206-0.0165-0.02570.1337-0.0053-0.00970.1581-0.00640.163489.202442.771270.1796
30.376-0.1621-0.1440.74370.05820.44130.0108-0.0090.0003-0.1085-0.0074-0.0019-0.07-0.01180.17810.0007-0.00470.1311-0.00120.138144.97462.158541.0087
40.5390.1314-0.21230.6731-0.02880.5555-0.020.0417-0.0743-0.0449-0.0105-0.0506-0.00910.02270.1812-0.00560.01110.1543-0.00260.170765.594535.767725.3338
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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