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- PDB-4bz9: Crystal structure of Schistosoma mansoni HDAC8 complexed with J1075 -

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Basic information

Entry
Database: PDB / ID: 4bz9
TitleCrystal structure of Schistosoma mansoni HDAC8 complexed with J1075
ComponentsHISTONE DEACETYLASE 8
KeywordsHYDROLASE / TRANSFERASE / PLATYHELMINTHS / EPIGENETICS / HDAC8
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 / : / 3-chlorobenzothiophene-2-carbohydroxamic acid / histone deacetylase
Similarity search - Component
Biological speciesSCHISTOSOMA MANSONI (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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)204,79832
Polymers201,7804
Non-polymers3,01928
Water11,385632
1
A: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1177
Polymers50,4451
Non-polymers6726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1367
Polymers50,4451
Non-polymers6916
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2639
Polymers50,4451
Non-polymers8188
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2829
Polymers50,4451
Non-polymers8378
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.280, 70.316, 98.130
Angle α, β, γ (deg.)77.93, 75.59, 85.54
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 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

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Non-polymers , 6 types, 660 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-KMY / 3-chlorobenzothiophene-2-carbohydroxamic acid


Mass: 227.667 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H6ClNO2S
#5: Chemical
ChemComp-DMF / DIMETHYLFORMAMIDE


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / Source method: isolated from a natural source / Formula: H2O

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Details

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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9537
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 116716 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Biso Wilson estimate: 22.31 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 17.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4.6 / % possible all: 95.6

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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→20.16 Å / Cor.coef. Fo:Fc: 0.9231 / Cor.coef. Fo:Fc free: 0.9002 / SU R Cruickshank DPI: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.175 / SU Rfree Blow DPI: 0.149 / SU Rfree Cruickshank DPI: 0.153
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN K. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=13744. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN K. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=13744. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=12.
RfactorNum. reflection% reflectionSelection details
Rfree0.2212 5913 5.07 %RANDOM
Rwork0.1908 ---
obs0.1923 116580 97.11 %-
Displacement parametersBiso mean: 24.92 Å2
Baniso -1Baniso -2Baniso -3
1-3.3855 Å2-4.1211 Å23.5353 Å2
2---3.7716 Å2-0.6241 Å2
3---0.3861 Å2
Refine analyzeLuzzati coordinate error obs: 0.234 Å
Refinement stepCycle: LAST / Resolution: 2→20.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12947 0 166 632 13745
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113475HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9518322HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4429SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes289HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1966HARMONIC5
X-RAY DIFFRACTIONt_it13475HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.05
X-RAY DIFFRACTIONt_other_torsion17.32
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1672SEMIHARMONIC5
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_contact16800SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2206 425 5.03 %
Rwork0.1848 8018 -
all0.1866 8443 -
obs--97.11 %
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)
10.98670.0855-0.14570.6718-0.390.9031-0.0086-0.113-0.05950.0677-0.028-0.06520.02830.04430.0365-0.0221-0.03460.0356-0.0592-0.003-0.107553.968324.788186.1068
20.6428-0.0918-0.04290.4488-0.14420.5320.0155-0.02480.04330.0191-0.0214-0.006-0.04890.01250.0060.0048-0.02350.0391-0.0544-0.008-0.076588.471243.339769.8104
30.4412-0.0799-0.13740.87130.01960.527-0.0272-0.0051-0.0223-0.08920.02560.0245-0.0164-0.05080.00160.031-0.02890.0415-0.0894-0.004-0.085544.43212.416841.0461
40.57580.0501-0.22240.8614-0.03380.7739-0.0420.0547-0.0674-0.0686-0.0004-0.05860.02870.05190.04240.0344-0.04150.0592-0.1029-0.0068-0.095565.270935.582825.1385
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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