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- PDB-4bz8: Crystal structure of Schistosoma mansoni HDAC8 complexed with J1038 -

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Basic information

Entry
Database: PDB / ID: 4bz8
TitleCrystal structure of Schistosoma mansoni HDAC8 complexed with J1038
ComponentsHISTONE DEACETYLASE 8
KeywordsHYDROLASE / PLATYHELMINTHS / HDAC8 / INHIBITOR
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-J38 / : / histone deacetylase
Similarity search - Component
Biological speciesSCHISTOSOMA MANSONI (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsMarek, M. / Romier, C.
CitationJournal: Plos Pathog. / Year: 2013
Title: Structural Basis for the Inhibition of Histone Deacetylase 8 (Hdac8), a Key Epigenetic Player in the Blood Fluke Schistosoma Mansoni.
Authors: Marek, M. / Kannan, S. / Hauser, A. / Moraes Mourao, M. / Caby, S. / Cura, V. / Stolfa, D.A. / Schmidtkunz, K. / Lancelot, J. / Andrade, L. / Renaud, J. / Oliveira, G. / Sippl, W. / Jung, M. ...Authors: Marek, M. / Kannan, S. / Hauser, A. / Moraes Mourao, M. / Caby, S. / Cura, V. / Stolfa, D.A. / Schmidtkunz, K. / Lancelot, J. / Andrade, L. / Renaud, J. / Oliveira, G. / Sippl, W. / Jung, M. / Cavarelli, J. / Pierce, R.J. / Romier, C.
History
DepositionJul 24, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HISTONE DEACETYLASE 8
B: HISTONE DEACETYLASE 8
C: HISTONE DEACETYLASE 8
D: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,30720
Polymers201,7804
Non-polymers1,52716
Water9,926551
1
A: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8275
Polymers50,4451
Non-polymers3824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8275
Polymers50,4451
Non-polymers3824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8275
Polymers50,4451
Non-polymers3824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8275
Polymers50,4451
Non-polymers3824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.655, 70.721, 98.391
Angle α, β, γ (deg.)77.98, 75.51, 85.80
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
HISTONE DEACETYLASE 8


Mass: 50444.875 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHISTOSOMA MANSONI (invertebrata) / Plasmid: PNEA/TH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5H660
#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-J38 / (2R)-2-methyl-3-oxo-4H-1,4-benzothiazine-6-carbohydroxamic acid


Mass: 238.263 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H10N2O3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 551 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE GSLVPR MOTIF AT THE END OF THE SEQUENCE CORRESPONDS TO A BAMHI CLONING SITE (GS) FOLLOWED BY A ...THE GSLVPR MOTIF AT THE END OF THE SEQUENCE CORRESPONDS TO A BAMHI CLONING SITE (GS) FOLLOWED BY A THROMBIN SITE (LVPR) THAT HAS BEEN CUT AFTER THE ARGININE.

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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: 1.5 Å3/Da / Density % sol: 19 % / Description: NONE
Crystal growDetails: 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: ID23-1 / Wavelength: 1.0723
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 84242 / % possible obs: 93.3 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Biso Wilson estimate: 26.35 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.7
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.9 / % possible all: 93.1

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T67

1t67


Resolution: 2.21→32.36 Å / Cor.coef. Fo:Fc: 0.9274 / Cor.coef. Fo:Fc free: 0.8947 / SU R Cruickshank DPI: 0.269 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.255 / SU Rfree Blow DPI: 0.195 / SU Rfree Cruickshank DPI: 0.201
RfactorNum. reflection% reflectionSelection details
Rfree0.2221 4283 5.09 %RANDOM
Rwork0.1777 ---
obs0.18 84066 93.16 %-
Displacement parametersBiso mean: 26.16 Å2
Baniso -1Baniso -2Baniso -3
1--2.8548 Å2-1.9143 Å2-2.2057 Å2
2---3.6389 Å2-3.4798 Å2
3---6.4937 Å2
Refine analyzeLuzzati coordinate error obs: 0.262 Å
Refinement stepCycle: LAST / Resolution: 2.21→32.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12883 0 76 551 13510
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113310HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9718105HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4406SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes285HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1941HARMONIC5
X-RAY DIFFRACTIONt_it13310HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion17.36
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1663SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact15404SEMIHARMONIC4
LS refinement shellResolution: 2.21→2.27 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2573 321 5.4 %
Rwork0.2074 5627 -
all0.2102 5948 -
obs--93.16 %
Refinement TLS params.Method: refined / Origin x: 63.0938 Å / Origin y: 26.6385 Å / Origin z: 55.5001 Å
111213212223313233
T-0.0296 Å20.0498 Å20.025 Å2--0.1181 Å2-0.0655 Å2--0.0102 Å2
L0.2264 °20.0791 °20.02 °2-0.114 °2-0.002 °2--0.0901 °2
S0.0001 Å °-0.0535 Å °-0.0133 Å °-0.0162 Å °-0.0039 Å °-0.0339 Å °0.0162 Å °0.0173 Å °0.0039 Å °
Refinement TLS groupSelection details: ALL

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