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- PDB-6hu1: Crystal structure of Schistosoma mansoni HDAC8 complexed with a b... -

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Basic information

Entry
Database: PDB / ID: 6hu1
TitleCrystal structure of Schistosoma mansoni HDAC8 complexed with a benzohydroxamate inhibitor 10
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-GT2 / : / histone deacetylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.996 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 5, 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
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.pdbx_ptnr1_label_alt_id / _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)207,10956
Polymers202,3324
Non-polymers4,77752
Water14,178787
1
A: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,69013
Polymers50,5831
Non-polymers1,10712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,76314
Polymers50,5831
Non-polymers1,18013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,80114
Polymers50,5831
Non-polymers1,21813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,85515
Polymers50,5831
Non-polymers1,27214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.220, 71.190, 99.030
Angle α, β, γ (deg.)78.27, 75.65, 85.73
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, 839 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-GT2 / 4-chloranyl-3-[(2,4-dichlorophenyl)carbonylamino]-~{N}-oxidanyl-benzamide


Mass: 359.592 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H9Cl3N2O3
#5: Chemical...
ChemComp-DMF / DIMETHYLFORMAMIDE


Mass: 73.094 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C3H7NO
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 787 / 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: 2.32 Å3/Da / Density % sol: 46.87 %
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: ID30B / Wavelength: 0.976252 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976252 Å / Relative weight: 1
ReflectionResolution: 1.996→48.42 Å / Num. obs: 120126 / % possible obs: 95.84 % / Redundancy: 3.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.1075 / Net I/σ(I): 8.67
Reflection shellResolution: 1.996→2.068 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.7312 / Mean I/σ(I) obs: 1.64 / Num. unique obs: 11466 / CC1/2: 0.653 / % possible all: 91.52

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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: 1.996→47.084 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 21.14
RfactorNum. reflection% reflection
Rfree0.2052 6006 5 %
Rwork0.1599 --
obs0.1622 120102 95.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.996→47.084 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13169 0 24 787 13980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113566
X-RAY DIFFRACTIONf_angle_d0.96718411
X-RAY DIFFRACTIONf_dihedral_angle_d14.1297902
X-RAY DIFFRACTIONf_chiral_restr0.0581954
X-RAY DIFFRACTIONf_plane_restr0.0062436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9956-2.01820.3291710.28873248X-RAY DIFFRACTION81
2.0182-2.0420.31421980.26183760X-RAY DIFFRACTION95
2.042-2.06690.28681970.24033739X-RAY DIFFRACTION94
2.0669-2.09310.30282030.23633842X-RAY DIFFRACTION95
2.0931-2.12060.30121920.2213678X-RAY DIFFRACTION95
2.1206-2.14960.27982010.21873816X-RAY DIFFRACTION95
2.1496-2.18040.26761990.2173771X-RAY DIFFRACTION95
2.1804-2.21290.25911990.18763791X-RAY DIFFRACTION95
2.2129-2.24750.24571990.17783767X-RAY DIFFRACTION95
2.2475-2.28430.21642000.16493801X-RAY DIFFRACTION96
2.2843-2.32370.22281940.16883696X-RAY DIFFRACTION93
2.3237-2.3660.2312010.15563807X-RAY DIFFRACTION95
2.366-2.41150.20541980.15453766X-RAY DIFFRACTION96
2.4115-2.46070.22292030.14943859X-RAY DIFFRACTION96
2.4607-2.51420.21322000.15873799X-RAY DIFFRACTION97
2.5142-2.57270.23112020.1573836X-RAY DIFFRACTION96
2.5727-2.6370.20642030.15363872X-RAY DIFFRACTION97
2.637-2.70830.21732030.15313853X-RAY DIFFRACTION97
2.7083-2.7880.22132040.15263873X-RAY DIFFRACTION98
2.788-2.8780.22322050.14433894X-RAY DIFFRACTION98
2.878-2.98080.17232020.14173842X-RAY DIFFRACTION96
2.9808-3.10010.17652060.14333903X-RAY DIFFRACTION97
3.1001-3.24120.17912040.14253874X-RAY DIFFRACTION98
3.2412-3.4120.18532030.14933872X-RAY DIFFRACTION98
3.412-3.62570.20772030.14773851X-RAY DIFFRACTION98
3.6257-3.90550.17552050.1423901X-RAY DIFFRACTION98
3.9055-4.29830.16412020.13883831X-RAY DIFFRACTION97
4.2983-4.91970.18422010.13523824X-RAY DIFFRACTION96
4.9197-6.19610.16812040.16723870X-RAY DIFFRACTION97
6.1961-47.0970.18842040.17193860X-RAY DIFFRACTION97
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)
10.62660.1515-0.11330.3992-0.09020.46580.0111-0.022-0.03290.0257-0.0352-0.01650.01160.00330.0788-0.0062-0.00340.11010.0060.094653.494925.407386.3371
20.6462-0.15860.05390.3584-0.03590.51380.0227-0.00420.0334-0.0034-0.0335-0.0121-0.0227-0.01410.08760.0037-0.00170.1143-0.00450.116888.894343.373170.4968
30.3094-0.0411-0.00880.7353-0.06230.4116-0.0486-0.0067-0.016-0.06570.04840.0287-0.0055-0.02750.1402-0.0002-0.00310.1078-0.00390.122644.94862.170540.7343
40.36610.1391-0.14130.5116-0.02140.4851-0.00540.0147-0.0146-0.0092-0.0064-0.0011-0.01280.030.1217-0.00460.00030.1006-0.00240.105864.614936.121724.9484
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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