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- PDB-6hsg: Crystal structure of Schistosoma mansoni HDAC8 H292M mutant compl... -

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Basic information

Entry
Database: PDB / ID: 6hsg
TitleCrystal structure of Schistosoma mansoni HDAC8 H292M mutant complexed with NCC-149
ComponentsHistone deacetylase
KeywordsHYDROLASE / Epigenetics / Histone deacetylase / HDAC8 / Selective inhibitor / Pathogen
Function / homology
Function and homology information


histone deacetylase / chromatin organization / 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-GM5 / : / histone deacetylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.846 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 14, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.3Nov 28, 2018Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)206,07144
Polymers202,3044
Non-polymers3,76740
Water16,394910
1
A: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,50411
Polymers50,5761
Non-polymers92810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,46910
Polymers50,5761
Non-polymers8929
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,66913
Polymers50,5761
Non-polymers1,09312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,43110
Polymers50,5761
Non-polymers8549
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.800, 70.830, 98.350
Angle α, β, γ (deg.)78.31, 75.80, 85.98
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: 50576.078 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, 950 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-GM5 / ~{N}-oxidanyl-3-[1-(phenylsulfanylmethyl)-1,2,3-triazol-4-yl]benzamide


Mass: 326.373 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H14N4O2S
#5: Chemical
ChemComp-DMF / DIMETHYLFORMAMIDE / Dimethylformamide


Mass: 73.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H7NO
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 910 / 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: 2.31 Å3/Da / Density % sol: 46.84 %
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: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Nov 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.846→43.48 Å / Num. obs: 151492 / % possible obs: 97.2 % / Redundancy: 3.6 % / CC1/2: 0.989 / Rmerge(I) obs: 0.1548 / Net I/σ(I): 5.5
Reflection shellResolution: 1.846→1.912 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.7932 / Mean I/σ(I) obs: 1.37 / Num. unique obs: 14080 / CC1/2: 0.465 / % possible all: 89.93

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementResolution: 1.846→43.48 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.95 / Phase error: 27.33
RfactorNum. reflection% reflection
Rfree0.2532 7574 5 %
Rwork0.2065 --
obs0.2088 151470 97.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.846→43.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12962 0 231 910 14103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813560
X-RAY DIFFRACTIONf_angle_d0.88718407
X-RAY DIFFRACTIONf_dihedral_angle_d13.6717959
X-RAY DIFFRACTIONf_chiral_restr0.0531965
X-RAY DIFFRACTIONf_plane_restr0.0062433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8458-1.86680.36461940.3163693X-RAY DIFFRACTION74
1.8668-1.88870.37272510.29674770X-RAY DIFFRACTION97
1.8887-1.91180.32322540.28314808X-RAY DIFFRACTION97
1.9118-1.9360.36472500.28534754X-RAY DIFFRACTION97
1.936-1.96140.31792550.28064845X-RAY DIFFRACTION97
1.9614-1.98830.34112510.27184779X-RAY DIFFRACTION97
1.9883-2.01670.31682540.25564816X-RAY DIFFRACTION97
2.0167-2.04680.28362520.2414791X-RAY DIFFRACTION97
2.0468-2.07880.27152550.22764852X-RAY DIFFRACTION98
2.0788-2.11290.30082490.22654746X-RAY DIFFRACTION97
2.1129-2.14930.29572570.23784869X-RAY DIFFRACTION98
2.1493-2.18840.31362520.22574803X-RAY DIFFRACTION98
2.1884-2.23050.26882550.21974842X-RAY DIFFRACTION98
2.2305-2.2760.28272530.21694807X-RAY DIFFRACTION98
2.276-2.32550.25512550.22114840X-RAY DIFFRACTION98
2.3255-2.37960.29192550.21394841X-RAY DIFFRACTION98
2.3796-2.43910.23752550.20664850X-RAY DIFFRACTION98
2.4391-2.5050.2792540.21664814X-RAY DIFFRACTION98
2.505-2.57870.26432550.21954854X-RAY DIFFRACTION98
2.5787-2.6620.26482560.21324868X-RAY DIFFRACTION98
2.662-2.75710.25472540.20844825X-RAY DIFFRACTION98
2.7571-2.86750.282560.21184868X-RAY DIFFRACTION98
2.8675-2.99790.2692570.20174871X-RAY DIFFRACTION99
2.9979-3.15590.24562560.1984870X-RAY DIFFRACTION99
3.1559-3.35360.24962580.19554893X-RAY DIFFRACTION99
3.3536-3.61240.23992540.1854832X-RAY DIFFRACTION98
3.6124-3.97570.20352580.17254910X-RAY DIFFRACTION99
3.9757-4.55050.19262540.15764820X-RAY DIFFRACTION98
4.5505-5.73120.20742570.17434878X-RAY DIFFRACTION99
5.7312-43.78950.20682580.1984887X-RAY DIFFRACTION99
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)
10.71390.1378-0.27130.3423-0.1070.5030.0203-0.0542-0.02280.0092-0.0238-0.01350.03860.079-0.00290.064-0.0099-0.01560.08710.00360.061452.995725.072586.159
20.7046-0.1260.11320.4178-0.01050.51120.0085-0.05220.0069-0.0175-0.01370.00280.0018-0.00890.09950.02730.00520.00040.0613-0.00190.054988.093143.271370.4907
30.352-0.0348-0.06150.72720.07550.469-0.00980.0182-0.0108-0.09350.0017-0.0151-0.0065-0.01450.08790.08540.0059-0.00410.04320.00570.062744.48882.469740.8987
40.39320.0952-0.12410.6105-0.16080.4140.00390.0145-0.0295-0.0345-0.0171-0.00630.02580.03640.00010.0733-0.00880.01080.0563-0.01090.057864.813836.362525.3246
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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