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

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Basic information

Entry
Database: PDB / ID: 6htz
TitleCrystal structure of Schistosoma mansoni HDAC8 complexed with a benzohydroxamate inhibitor 8
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-GRK / : / histone deacetylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.841 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 ...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 1.3Jan 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)206,48851
Polymers202,3324
Non-polymers4,15647
Water17,997999
1
A: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,48511
Polymers50,5831
Non-polymers90110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,77715
Polymers50,5831
Non-polymers1,19414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,57712
Polymers50,5831
Non-polymers99411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,65013
Polymers50,5831
Non-polymers1,06712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.260, 71.260, 99.070
Angle α, β, γ (deg.)77.90, 75.53, 85.44
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, 1046 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-GRK / 4-methoxy-~{N}-oxidanyl-3-(2-phenylethanoylamino)benzamide


Mass: 300.309 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H16N2O4
#5: Chemical...
ChemComp-DMF / DIMETHYLFORMAMIDE


Mass: 73.094 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C3H7NO
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 999 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
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: 1.841→48.33 Å / Num. obs: 149080 / % possible obs: 93.25 % / Redundancy: 3.3 % / CC1/2: 0.985 / Rmerge(I) obs: 0.1546 / Net I/σ(I): 8.4
Reflection shellResolution: 1.841→1.907 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.9096 / Num. unique obs: 13893 / CC1/2: 0.55 / Rsym value: 1.51 / % possible all: 86.82

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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: 1.841→48.32 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 23.42
RfactorNum. reflection% reflection
Rfree0.2182 7446 5 %
Rwork0.1769 --
obs0.179 149024 93.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.841→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13017 0 261 999 14277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813676
X-RAY DIFFRACTIONf_angle_d0.84218569
X-RAY DIFFRACTIONf_dihedral_angle_d13.5868013
X-RAY DIFFRACTIONf_chiral_restr0.0541983
X-RAY DIFFRACTIONf_plane_restr0.0062439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.841-1.86190.47831900.44353613X-RAY DIFFRACTION71
1.8619-1.88380.37592530.29984797X-RAY DIFFRACTION95
1.8838-1.90680.3322520.26944784X-RAY DIFFRACTION94
1.9068-1.93090.29952500.24544759X-RAY DIFFRACTION94
1.9309-1.95630.28112360.22694467X-RAY DIFFRACTION89
1.9563-1.98310.2692520.21444787X-RAY DIFFRACTION93
1.9831-2.01150.25452460.20684688X-RAY DIFFRACTION94
2.0115-2.04150.27232500.21274734X-RAY DIFFRACTION93
2.0415-2.07340.27222490.21194743X-RAY DIFFRACTION95
2.0734-2.10740.25992550.21444843X-RAY DIFFRACTION94
2.1074-2.14370.23452490.18974766X-RAY DIFFRACTION94
2.1437-2.18270.22022510.18844759X-RAY DIFFRACTION94
2.1827-2.22470.22492520.18224799X-RAY DIFFRACTION93
2.2247-2.27010.25832470.18724683X-RAY DIFFRACTION94
2.2701-2.31950.21492480.18294733X-RAY DIFFRACTION94
2.3195-2.37340.24652530.18274811X-RAY DIFFRACTION94
2.3734-2.43280.23872450.1784681X-RAY DIFFRACTION93
2.4328-2.49860.2282420.17364600X-RAY DIFFRACTION92
2.4986-2.57210.21712540.18184814X-RAY DIFFRACTION95
2.5721-2.65510.23292500.17674769X-RAY DIFFRACTION94
2.6551-2.750.22722520.18154807X-RAY DIFFRACTION95
2.75-2.86010.23552540.17614822X-RAY DIFFRACTION95
2.8601-2.99020.20792530.16454820X-RAY DIFFRACTION95
2.9902-3.14780.20742510.16654767X-RAY DIFFRACTION95
3.1478-3.3450.18242530.16124792X-RAY DIFFRACTION94
3.345-3.60320.19712480.15474712X-RAY DIFFRACTION93
3.6032-3.96570.17082510.14354771X-RAY DIFFRACTION94
3.9657-4.53910.16312540.13124840X-RAY DIFFRACTION96
4.5391-5.71740.16462530.14614807X-RAY DIFFRACTION95
5.7174-48.3370.20342530.17744810X-RAY DIFFRACTION95
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)
10.59460.1454-0.2170.346-0.22380.44840.0123-0.0622-0.02910.0126-0.035-0.0282-0.00030.0278-0.00320.0575-0.0113-0.01020.11-0.00240.075853.320625.478286.064
20.5083-0.06990.03650.3027-0.06380.30710.0113-0.01870.0207-0.0199-0.0251-0.016-0.0252-0.00490.00010.06340.007-0.00430.08530.00110.081888.647743.787470.2514
30.3449-0.0507-0.09740.7690.08540.3367-0.0286-0.013-0.01-0.07310.0210.0348-0.0193-0.03120.04260.07580.0053-0.00810.04380.00440.052944.07892.673140.7593
40.4030.2103-0.22790.64290.00650.4094-0.05430.0198-0.0848-0.07450.0277-0.03850.0010.0233-0.00160.1118-0.00660.01030.0743-0.00790.081864.816936.27924.9206
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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