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

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Basic information

Entry
Database: PDB / ID: 6htt
TitleCrystal structure of Schistosoma mansoni HDAC8 complexed with a benzohydroxamate inhibitor 7
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-GQZ / : / histone deacetylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.748 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 4, 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)207,74767
Polymers202,3324
Non-polymers5,41563
Water24,5901365
1
A: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,66313
Polymers50,5831
Non-polymers1,08012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,86316
Polymers50,5831
Non-polymers1,28015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,21220
Polymers50,5831
Non-polymers1,62919
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,00918
Polymers50,5831
Non-polymers1,42617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.400, 70.500, 98.330
Angle α, β, γ (deg.)75.80, 77.71, 85.53
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, 1428 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-GQZ / ~{N}1-oxidanyl-~{N}3-phenyl-benzene-1,3-dicarboxamide


Mass: 256.257 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H12N2O3
#5: Chemical...
ChemComp-DMF / DIMETHYLFORMAMIDE


Mass: 73.094 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C3H7NO
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1365 / 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: 2.22 Å3/Da / Density % sol: 44.56 %
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: 0.97779 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97779 Å / Relative weight: 1
ReflectionResolution: 1.748→47.82 Å / Num. obs: 169968 / % possible obs: 93.81 % / Redundancy: 1.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.04169 / Net I/σ(I): 11.8
Reflection shellResolution: 1.748→1.811 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.2942 / Mean I/σ(I) obs: 2.32 / Num. unique obs: 16485 / CC1/2: 0.822 / % possible all: 90.67

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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: 1.748→47.82 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 17.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.183 8498 5 %
Rwork0.1498 --
obs0.1514 169960 93.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.748→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12945 0 343 1365 14653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613689
X-RAY DIFFRACTIONf_angle_d0.79818565
X-RAY DIFFRACTIONf_dihedral_angle_d12.4618001
X-RAY DIFFRACTIONf_chiral_restr0.0531974
X-RAY DIFFRACTIONf_plane_restr0.0062431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7477-1.76750.3212480.27264718X-RAY DIFFRACTION81
1.7675-1.78830.27752800.22675336X-RAY DIFFRACTION94
1.7883-1.81010.25872890.20375494X-RAY DIFFRACTION94
1.8101-1.8330.26572800.2115305X-RAY DIFFRACTION94
1.833-1.85720.24872890.20265506X-RAY DIFFRACTION95
1.8572-1.88260.25572850.1875399X-RAY DIFFRACTION95
1.8826-1.90950.22392890.17455504X-RAY DIFFRACTION95
1.9095-1.9380.23022820.16785356X-RAY DIFFRACTION94
1.938-1.96830.19842850.16425408X-RAY DIFFRACTION94
1.9683-2.00060.1962900.15915511X-RAY DIFFRACTION95
2.0006-2.03510.19342860.15535431X-RAY DIFFRACTION95
2.0351-2.07210.19692870.15635468X-RAY DIFFRACTION95
2.0721-2.11190.19292850.16095404X-RAY DIFFRACTION95
2.1119-2.1550.21172860.15035446X-RAY DIFFRACTION95
2.155-2.20190.17412870.13865444X-RAY DIFFRACTION94
2.2019-2.25310.17532840.14445395X-RAY DIFFRACTION95
2.2531-2.30940.18432860.14495426X-RAY DIFFRACTION95
2.3094-2.37190.18612850.14535424X-RAY DIFFRACTION94
2.3719-2.44170.18912870.14175453X-RAY DIFFRACTION95
2.4417-2.52050.18772890.14715488X-RAY DIFFRACTION95
2.5205-2.61060.17452850.1485413X-RAY DIFFRACTION95
2.6106-2.71510.21142870.14925449X-RAY DIFFRACTION94
2.7151-2.83860.17972810.14465350X-RAY DIFFRACTION94
2.8386-2.98830.17082840.14375389X-RAY DIFFRACTION94
2.9883-3.17550.17272830.1435378X-RAY DIFFRACTION93
3.1755-3.42060.17222800.14055329X-RAY DIFFRACTION93
3.4206-3.76470.16012770.13185249X-RAY DIFFRACTION91
3.7647-4.30910.14342770.12345262X-RAY DIFFRACTION92
4.3091-5.42780.14592820.13225360X-RAY DIFFRACTION93
5.4278-47.8380.18362830.1685367X-RAY DIFFRACTION94
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)
10.79960.2513-0.07510.3648-0.16740.43320.0393-0.1156-0.05430.0101-0.0766-0.04940.01410.0167-0.00620.0855-0.008-0.00520.150.01260.10653.701425.787686.0297
20.6278-0.11860.10120.2454-0.05110.33070.017-0.05450.0275-0.0247-0.0154-0.016-0.0255-0.01620.00260.07070.00830.00240.095-0.0070.085788.495443.494570.1203
30.256-0.0644-0.02270.55370.05760.3292-0.0276-0.01-0.0114-0.040.00960.01250.0008-0.021-00.11980.00440.00390.0826-0.00440.104144.26792.503740.8505
40.34240.0929-0.22330.5671-0.14760.5636-0.02610.0147-0.0098-0.05770.016-0.0250.0320.0028-0.00010.136-0.0115-0.00550.0848-0.00390.10464.97435.911825.2444
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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