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

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Basic information

Entry
Database: PDB / ID: 6hsf
TitleCrystal structure of Schistosoma mansoni HDAC8 mutant H292M complexed with PCI-34051
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-GKW / : / histone deacetylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 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
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)205,87843
Polymers202,3044
Non-polymers3,57439
Water14,358797
1
A: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,63913
Polymers50,5761
Non-polymers1,06312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3089
Polymers50,5761
Non-polymers7328
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,58512
Polymers50,5761
Non-polymers1,00911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3469
Polymers50,5761
Non-polymers7708
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.600, 70.670, 98.170
Angle α, β, γ (deg.)75.83, 78.25, 86.05
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, 836 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-GKW / 1-[(4-methoxyphenyl)methyl]-~{N}-oxidanyl-indole-6-carboxamide


Mass: 296.321 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H16N2O3
#5: Chemical
ChemComp-DMF / DIMETHYLFORMAMIDE


Mass: 73.094 Da / Num. of mol.: 16 / 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.: 797 / 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: 2.3 Å3/Da / Density % sol: 46.47 %
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: 1.899→43.37 Å / Num. obs: 138765 / % possible obs: 97.58 % / Redundancy: 3.6 % / CC1/2: 0.993 / Rmerge(I) obs: 0.1536 / Net I/σ(I): 6.6
Reflection shellResolution: 1.899→1.967 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.087 / Mean I/σ(I) obs: 1.08 / Num. unique obs: 13322 / CC1/2: 0.445 / % possible all: 93.22

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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: 1.899→43.37 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.95 / Phase error: 28.15
RfactorNum. reflection% reflection
Rfree0.2651 6935 5 %
Rwork0.2108 --
obs0.2136 138739 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.899→43.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12798 0 222 797 13817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913443
X-RAY DIFFRACTIONf_angle_d1.00118261
X-RAY DIFFRACTIONf_dihedral_angle_d14.1017826
X-RAY DIFFRACTIONf_chiral_restr0.0571947
X-RAY DIFFRACTIONf_plane_restr0.0072335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8991-1.92070.36742020.32423854X-RAY DIFFRACTION85
1.9207-1.94330.33482290.29724351X-RAY DIFFRACTION97
1.9433-1.9670.34052350.28314450X-RAY DIFFRACTION97
1.967-1.99190.3452250.2824289X-RAY DIFFRACTION97
1.9919-2.01810.34492350.27694457X-RAY DIFFRACTION97
2.0181-2.04570.32482290.26934347X-RAY DIFFRACTION97
2.0457-2.07490.32972330.24724438X-RAY DIFFRACTION98
2.0749-2.10590.29282280.24994346X-RAY DIFFRACTION98
2.1059-2.13880.30972340.24834439X-RAY DIFFRACTION98
2.1388-2.17390.29922270.24384315X-RAY DIFFRACTION98
2.1739-2.21140.28052350.23314464X-RAY DIFFRACTION98
2.2114-2.25160.28462290.22874369X-RAY DIFFRACTION98
2.2516-2.29490.29432340.23724440X-RAY DIFFRACTION98
2.2949-2.34170.30572290.23524360X-RAY DIFFRACTION98
2.3417-2.39260.29872310.23284390X-RAY DIFFRACTION98
2.3926-2.44830.28152340.22464441X-RAY DIFFRACTION98
2.4483-2.50950.28462340.22434436X-RAY DIFFRACTION98
2.5095-2.57740.26322320.21074405X-RAY DIFFRACTION98
2.5774-2.65320.26962330.21484436X-RAY DIFFRACTION98
2.6532-2.73880.27832330.20844419X-RAY DIFFRACTION98
2.7388-2.83670.28412320.21254411X-RAY DIFFRACTION98
2.8367-2.95020.26682340.20784461X-RAY DIFFRACTION98
2.9502-3.08450.27972330.20184409X-RAY DIFFRACTION98
3.0845-3.2470.23322330.19814431X-RAY DIFFRACTION99
3.247-3.45040.26642320.19714422X-RAY DIFFRACTION98
3.4504-3.71670.23612340.18994443X-RAY DIFFRACTION99
3.7167-4.09050.22122340.16914445X-RAY DIFFRACTION99
4.0905-4.68180.22722340.16254449X-RAY DIFFRACTION99
4.6818-5.89630.2132350.18614450X-RAY DIFFRACTION99
5.8963-43.69790.24162330.20534437X-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)
10.46780.027-0.08360.316-0.10130.3821-0.0155-0.0194-0.040.0202-0.0083-0.04930.0328-0.001200.057-0.0067-0.01070.07550.01020.074453.761325.056585.6934
20.5565-0.13060.00670.23560.00230.30120.026-0.04260.0084-0.0026-0.0248-0.0175-0.0159-0.0118-0.00040.03980.00840.00150.0726-0.00210.047188.954743.239169.8914
30.3051-0.0265-0.12780.55330.11540.266-0.0179-0.0022-0.0016-0.01080.01830.02390.0066-0.01050.00690.07040.0053-0.00240.03770.00410.059445.02792.089240.6354
40.29560.1038-0.22270.3352-0.11080.3549-0.0220.0258-0.0332-0.0010.0119-0.01260.03760.008-00.0583-0.01380.00260.0436-0.0090.045665.360336.121924.7877
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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