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- PDB-6hqy: Crystal structure of Schistosoma mansoni HDAC8 complexed with PCI... -

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Basic information

Entry
Database: PDB / ID: 6hqy
TitleCrystal structure of Schistosoma mansoni HDAC8 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
Chem-GKW / : / histone deacetylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 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
DepositionSep 25, 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)204,64426
Polymers202,3324
Non-polymers2,31222
Water3,549197
1
A: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2998
Polymers50,5831
Non-polymers7167
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1156
Polymers50,5831
Non-polymers5325
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1156
Polymers50,5831
Non-polymers5325
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1156
Polymers50,5831
Non-polymers5325
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.877, 71.053, 98.198
Angle α, β, γ (deg.)78.06, 75.61, 85.45
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, 219 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 110 K
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: 2.5→50 Å / Num. obs: 60928 / % possible obs: 97 % / Redundancy: 3.4 % / Rpim(I) all: 0.063 / Net I/σ(I): 8.36
Reflection shellResolution: 2.5→2.54 Å

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Processing

Software
NameVersionClassification
PHENIXdev_1796refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZ5

4bz5


Resolution: 2.501→42.76 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 27.54
RfactorNum. reflection% reflection
Rfree0.2535 3089 5.07 %
Rwork0.1804 --
obs0.1843 60906 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.501→42.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12890 0 136 197 13223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813385
X-RAY DIFFRACTIONf_angle_d1.03218195
X-RAY DIFFRACTIONf_dihedral_angle_d14.7134792
X-RAY DIFFRACTIONf_chiral_restr0.0411946
X-RAY DIFFRACTIONf_plane_restr0.0052318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5013-2.54040.33641290.24072529X-RAY DIFFRACTION91
2.5404-2.58210.3381540.21382554X-RAY DIFFRACTION96
2.5821-2.62660.31321510.19162609X-RAY DIFFRACTION96
2.6266-2.67430.26121360.17582586X-RAY DIFFRACTION96
2.6743-2.72580.27161550.17712621X-RAY DIFFRACTION97
2.7258-2.78140.31091450.18222569X-RAY DIFFRACTION97
2.7814-2.84190.27831350.18382673X-RAY DIFFRACTION96
2.8419-2.9080.25951380.17492581X-RAY DIFFRACTION97
2.908-2.98070.29531330.18452645X-RAY DIFFRACTION97
2.9807-3.06120.28321220.19062639X-RAY DIFFRACTION97
3.0612-3.15130.27311340.19012643X-RAY DIFFRACTION97
3.1513-3.2530.26271390.18932638X-RAY DIFFRACTION98
3.253-3.36920.26081230.19152683X-RAY DIFFRACTION97
3.3692-3.5040.28931370.18962621X-RAY DIFFRACTION97
3.504-3.66340.24621700.18012600X-RAY DIFFRACTION98
3.6634-3.85640.27841240.17472662X-RAY DIFFRACTION98
3.8564-4.09790.23081550.16842654X-RAY DIFFRACTION98
4.0979-4.4140.21031230.15942687X-RAY DIFFRACTION98
4.414-4.85760.20581330.15922638X-RAY DIFFRACTION98
4.8576-5.55920.22391520.17352649X-RAY DIFFRACTION98
5.5592-6.99910.23491550.19312683X-RAY DIFFRACTION99
6.9991-42.76640.20881460.17812653X-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)
10.48260.06110.04420.4472-0.17540.4026-0.0156-0.0119-0.0139-0.0032-0.01220.046-0.01830.0028-00.06670.0042-0.01150.10110.01410.082253.622425.180285.6142
20.6108-0.25060.03890.4875-0.05330.39440.0199-0.0403-0.0011-0.0146-0.0093-0.00010.0143-0.029500.04920.0038-0.00120.0876-0.01140.069688.810143.257570.3746
30.3977-0.0346-0.14230.82250.04610.4362-0.0111-0.0021-0.0242-0.08250.00410.0217-0.0250.0112-0.00080.0696-0.0041-0.01310.01560.0090.03944.46992.208940.779
40.4190.1024-0.16770.57030.05130.4264-0.02040.01780.0016-0.0246-0.0206-0.04550.01760.0239-00.0864-0.01430.01540.0807-0.0160.093265.071735.767625.3708
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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