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- PDB-6hu3: Crystal structure of Schistosoma mansoni HDAC8 complexed with a t... -

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Basic information

Entry
Database: PDB / ID: 6hu3
TitleCrystal structure of Schistosoma mansoni HDAC8 complexed with a triazole hydroxamate inhibitor
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
DIMETHYLFORMAMIDE / Chem-GRZ / : / histone deacetylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.655 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 / 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)206,29746
Polymers202,3324
Non-polymers3,96542
Water15,313850
1
A: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,62512
Polymers50,5831
Non-polymers1,04211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,60612
Polymers50,5831
Non-polymers1,02311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,53311
Polymers50,5831
Non-polymers95010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,53311
Polymers50,5831
Non-polymers95010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.640, 70.430, 97.920
Angle α, β, γ (deg.)75.48, 78.20, 86.17
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, 892 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-GRZ / 1-[5-chloranyl-2-(4-fluoranylphenoxy)phenyl]-~{N}-oxidanyl-1,2,3-triazole-4-carboxamide


Mass: 348.716 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H10ClFN4O3
#5: Chemical...
ChemComp-DMF / DIMETHYLFORMAMIDE


Mass: 73.094 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C3H7NO
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 850 / 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: 2.24 Å3/Da / Density % sol: 45.02 %
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: ID29 / Wavelength: 1.072522 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072522 Å / Relative weight: 1
ReflectionResolution: 1.655→48.95 Å / Num. obs: 196636 / % possible obs: 92.33 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04258 / Net I/σ(I): 14.93
Reflection shellResolution: 1.655→1.715 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.8857 / Mean I/σ(I) obs: 1.23 / Num. unique obs: 18437 / CC1/2: 0.509 / % possible all: 86.22

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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: 1.655→48.945 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 20.44
RfactorNum. reflection% reflection
Rfree0.1935 9832 5 %
Rwork0.1617 --
obs0.1633 196617 92.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.655→48.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13271 0 24 850 14145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813772
X-RAY DIFFRACTIONf_angle_d0.89818726
X-RAY DIFFRACTIONf_dihedral_angle_d13.6778066
X-RAY DIFFRACTIONf_chiral_restr0.0591993
X-RAY DIFFRACTIONf_plane_restr0.0062487
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6549-1.67370.39042500.38184763X-RAY DIFFRACTION70
1.6737-1.69340.36063250.33166156X-RAY DIFFRACTION91
1.6934-1.71410.3383290.31526256X-RAY DIFFRACTION92
1.7141-1.73580.31463270.29536213X-RAY DIFFRACTION93
1.7358-1.75860.3033270.26536225X-RAY DIFFRACTION91
1.7586-1.78270.30513250.2456170X-RAY DIFFRACTION91
1.7827-1.80820.24943260.21696192X-RAY DIFFRACTION91
1.8082-1.83520.26413190.20536067X-RAY DIFFRACTION91
1.8352-1.86380.24233220.18886112X-RAY DIFFRACTION91
1.8638-1.89440.22313100.18285888X-RAY DIFFRACTION87
1.8944-1.92710.21423310.18086279X-RAY DIFFRACTION93
1.9271-1.96210.20773340.17676352X-RAY DIFFRACTION93
1.9621-1.99980.20143310.186290X-RAY DIFFRACTION93
1.9998-2.04070.20813280.17696233X-RAY DIFFRACTION93
2.0407-2.0850.21143320.1626312X-RAY DIFFRACTION93
2.085-2.13350.17453330.16036317X-RAY DIFFRACTION93
2.1335-2.18690.19073270.15386211X-RAY DIFFRACTION92
2.1869-2.2460.18573210.15176098X-RAY DIFFRACTION91
2.246-2.31210.16843240.15636163X-RAY DIFFRACTION92
2.3121-2.38670.19923370.15746406X-RAY DIFFRACTION94
2.3867-2.4720.19693360.15756387X-RAY DIFFRACTION94
2.472-2.5710.20833370.16666395X-RAY DIFFRACTION94
2.571-2.6880.18943360.16026390X-RAY DIFFRACTION95
2.688-2.82970.18753330.16246318X-RAY DIFFRACTION94
2.8297-3.0070.17253310.15576283X-RAY DIFFRACTION93
3.007-3.23910.19613390.15856458X-RAY DIFFRACTION96
3.2391-3.5650.17143430.14956512X-RAY DIFFRACTION96
3.565-4.08060.17463370.13836396X-RAY DIFFRACTION95
4.0806-5.14030.16723390.12866443X-RAY DIFFRACTION95
5.1403-48.96650.19463430.16866500X-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)
10.81760.2015-0.04890.6833-0.21130.73580.0113-0.0354-0.04870.0732-0.0357-0.10340.0189-0.0163-00.2233-0.0073-0.01570.23140.02020.242953.707325.470185.5381
20.9024-0.21640.120.395-0.06430.54270.0185-0.0753-0.0101-0.0032-0.0297-0.0124-0.0233-0.022200.18670.00090.00460.2192-0.00470.192688.616542.975969.9117
30.3623-0.2651-0.06020.75470.15610.5738-0.01670.0054-0.0222-0.0295-0.00340.0539-0.0284-0.017500.1937-0.001-0.00470.1821-0.00290.212345.35552.490640.4898
40.5570.2765-0.30920.7851-0.13790.6897-0.03780.069-0.0443-0.05230.0285-0.02750.0256-0.033200.2392-0.01040.00270.2153-0.0160.208265.711936.217324.7814
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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