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

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Basic information

Entry
Database: PDB / ID: 6hsz
TitleCrystal structure of Schistosoma mansoni HDAC8 complexed with a benzohydroxamate inhibitor 2
ComponentsHistone deacetylase
KeywordsHYDROLASE / Epigenetics / Histone deacetylase / HDAC8 / Selective inhibitor / Pathogen
Function / homology
Function and homology information


histone deacetylase / histone deacetylase activity / negative regulation of transcription by RNA polymerase II / nucleus / 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
3-benzamido-4-methyl-~{N}-oxidanyl-benzamide / : / histone deacetylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.374 Å
AuthorsMarek, M. / Shaik, T.B. / 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 2, 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)204,63227
Polymers202,3324
Non-polymers2,30023
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-21 kcal/mol
Surface area64020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.774, 70.802, 98.343
Angle α, β, γ (deg.)77.85, 75.48, 85.28
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 , 5 types, 348 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-GOW / 3-benzamido-4-methyl-~{N}-oxidanyl-benzamide


Mass: 270.283 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H14N2O3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 325 / 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: 46.67 %
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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.374→34.97 Å / Num. obs: 69324 / % possible obs: 94.99 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 14.44
Reflection shellResolution: 2.374→2.459 Å / Num. unique obs: 6161 / % possible all: 84.13

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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: 2.374→34.968 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 22.55
RfactorNum. reflection% reflection
Rfree0.2196 3528 5.09 %
Rwork0.1587 --
obs0.1618 69306 94.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.374→34.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12939 0 134 325 13398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913459
X-RAY DIFFRACTIONf_angle_d0.98518297
X-RAY DIFFRACTIONf_dihedral_angle_d12.4117842
X-RAY DIFFRACTIONf_chiral_restr0.0531959
X-RAY DIFFRACTIONf_plane_restr0.0062337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3737-2.40620.26481020.16281802X-RAY DIFFRACTION66
2.4062-2.44060.28161330.17092673X-RAY DIFFRACTION96
2.4406-2.4770.26131530.18232596X-RAY DIFFRACTION95
2.477-2.51570.25781360.18422695X-RAY DIFFRACTION96
2.5157-2.55690.27781510.17592583X-RAY DIFFRACTION95
2.5569-2.6010.25191520.16782671X-RAY DIFFRACTION95
2.601-2.64830.251400.16832655X-RAY DIFFRACTION96
2.6483-2.69920.24621520.16482669X-RAY DIFFRACTION97
2.6992-2.75430.25271510.16562629X-RAY DIFFRACTION96
2.7543-2.81420.24841330.15962709X-RAY DIFFRACTION96
2.8142-2.87960.25121490.16572627X-RAY DIFFRACTION97
2.8796-2.95160.231360.16582707X-RAY DIFFRACTION96
2.9516-3.03130.2641210.16522672X-RAY DIFFRACTION96
3.0313-3.12050.24441300.16382663X-RAY DIFFRACTION96
3.1205-3.22110.2271500.16312717X-RAY DIFFRACTION97
3.2211-3.33620.23431330.16782654X-RAY DIFFRACTION96
3.3362-3.46960.22831270.17212666X-RAY DIFFRACTION96
3.4696-3.62740.22761730.15362676X-RAY DIFFRACTION97
3.6274-3.81840.19851310.15142694X-RAY DIFFRACTION97
3.8184-4.05730.20161570.14332638X-RAY DIFFRACTION96
4.0573-4.370.1871250.1352734X-RAY DIFFRACTION97
4.37-4.80880.18641340.13662669X-RAY DIFFRACTION96
4.8088-5.50230.18821500.14972666X-RAY DIFFRACTION97
5.5023-6.92350.19461640.16722661X-RAY DIFFRACTION97
6.9235-34.97170.19011450.16952652X-RAY DIFFRACTION96
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)
10.55540.104-0.06790.2209-0.22350.49120.0057-0.0614-0.02560.0072-0.02080.0090.01410.0444-00.1506-0.005-0.01330.1820.00670.156353.768325.10985.8213
20.6082-0.1493-0.05320.1711-0.07480.45450.0097-0.04010.0135-0.0227-0.0251-0.01530.00580.007100.1114-0.0026-0.00850.1303-0.00550.131688.667143.075970.4067
30.1816-0.093-0.15080.69950.04840.3842-0.0349-0.0163-0.0241-0.09030.0103-0.0011-0.0201-0.017900.14610.0016-0.01020.1177-0.00310.13144.55791.988340.8797
40.37590.1331-0.22990.58070.04020.4217-0.0270.0084-0.0384-0.05860.0177-0.0643-0.00510.003900.1655-0.01230.01880.1445-0.01190.156665.002535.456325.2989
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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