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- PDB-6hrq: Crystal structure of Schistosoma mansoni HDAC8 complexed with NCC-149 -

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Basic information

Entry
Database: PDB / ID: 6hrq
TitleCrystal structure of Schistosoma mansoni HDAC8 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 / MOLECULAR REPLACEMENT / Resolution: 1.845 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
DepositionSep 28, 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)207,45661
Polymers202,3324
Non-polymers5,12457
Water20,8971160
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16760 Å2
ΔGint48 kcal/mol
Surface area64720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.430, 71.480, 99.260
Angle α, β, γ (deg.)78.11, 75.54, 85.37
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, 1217 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.: 28 / 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.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1160 / 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: 46.88 %
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: ID30B / Wavelength: 0.9763 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: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.845→50 Å / Num. obs: 152133 / % possible obs: 95.11 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Net I/σ(I): 15.4
Reflection shellResolution: 1.845→1.9 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.78 / Num. unique obs: 14354 / CC1/2: 0.659 / % possible all: 89.64

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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: 1.845→47.158 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 18.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1832 7606 5 %
Rwork0.1498 --
obs0.1515 152126 94.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.845→47.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13079 0 322 1160 14561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813769
X-RAY DIFFRACTIONf_angle_d0.83218671
X-RAY DIFFRACTIONf_dihedral_angle_d13.4098062
X-RAY DIFFRACTIONf_chiral_restr0.0561986
X-RAY DIFFRACTIONf_plane_restr0.0062471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8445-1.86550.37332020.34333837X-RAY DIFFRACTION76
1.8655-1.88740.29962510.26784773X-RAY DIFFRACTION94
1.8874-1.91040.27332550.24534840X-RAY DIFFRACTION95
1.9104-1.93460.24882490.21044733X-RAY DIFFRACTION93
1.9346-1.96010.26932320.20294406X-RAY DIFFRACTION88
1.9601-1.98690.25722580.20324908X-RAY DIFFRACTION95
1.9869-2.01530.22522500.18764737X-RAY DIFFRACTION95
2.0153-2.04540.21912530.18514815X-RAY DIFFRACTION95
2.0454-2.07740.2262520.17164783X-RAY DIFFRACTION95
2.0774-2.11140.20592580.15934915X-RAY DIFFRACTION95
2.1114-2.14780.20172540.15314818X-RAY DIFFRACTION96
2.1478-2.18690.17832550.14674838X-RAY DIFFRACTION95
2.1869-2.22890.19652570.14354894X-RAY DIFFRACTION95
2.2289-2.27440.20632550.1474847X-RAY DIFFRACTION96
2.2744-2.32390.17452570.14274887X-RAY DIFFRACTION97
2.3239-2.3780.18522610.13994947X-RAY DIFFRACTION96
2.378-2.43740.17052550.14344847X-RAY DIFFRACTION97
2.4374-2.50330.18382530.14564802X-RAY DIFFRACTION95
2.5033-2.5770.19742600.1564949X-RAY DIFFRACTION97
2.577-2.66010.18862600.14754941X-RAY DIFFRACTION97
2.6601-2.75520.17832590.14994917X-RAY DIFFRACTION97
2.7552-2.86550.19312580.14294900X-RAY DIFFRACTION97
2.8655-2.99590.18412590.14174927X-RAY DIFFRACTION97
2.9959-3.15380.16532570.14724885X-RAY DIFFRACTION97
3.1538-3.35140.18372600.1434943X-RAY DIFFRACTION97
3.3514-3.61010.17572560.13724848X-RAY DIFFRACTION95
3.6101-3.97320.15492570.1294885X-RAY DIFFRACTION96
3.9732-4.54770.13772580.12224909X-RAY DIFFRACTION97
4.5477-5.7280.16582580.13444893X-RAY DIFFRACTION96
5.728-47.17360.16882570.16154896X-RAY DIFFRACTION97
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)
10.78530.1366-0.16130.4165-0.21210.5476-0.0023-0.0761-0.03030.0265-0.0255-0.04080.00420.0303-00.1502-0.0061-0.00970.1760.00110.161753.538525.436586.2645
20.6026-0.21870.04940.3074-0.06070.47870.0032-0.01410.0316-0.0012-0.0193-0.017-0.0132-0.021400.1409-0.0021-0.00250.1564-0.00260.163988.741643.763670.3439
30.2609-0.1075-0.07670.79340.00960.5568-0.0316-0.011-0.0153-0.06740.03040.0208-0.0234-0.026600.1472-0.0034-0.00690.12230.00040.135144.42722.763940.6611
40.39980.0022-0.24040.63520.08950.66-0.00890.0345-0.0468-0.0242-0.0136-0.0045-0.0170.036100.1621-0.0090.00190.1551-0.00340.151464.968336.362324.9245
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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