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- PDB-4cqf: Crystal structure of Schistosoma mansoni HDAC8 complexed with a m... -

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Basic information

Entry
Database: PDB / ID: 4cqf
TitleCrystal structure of Schistosoma mansoni HDAC8 complexed with a mercaptoacetamide inhibitor
ComponentsHISTONE DEACETYLASE 8
KeywordsHYDROLASE / STRUCTURAL PROTEIN / EUKARYOTES / PLATYHELMINTHS / EPIGENETICS / HISTONE DEACETYLASES / INHIBITION
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
6-(2-Mercaptoacetylamino)-N-phenylhexanamide / DIMETHYLFORMAMIDE / : / histone deacetylase
Similarity search - Component
Biological speciesSCHISTOSOMA MANSONI (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMarek, M. / Romier, C.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Molecular Basis for the Anti-Parasitic Activity of a Mercaptoacetamide Derivative that Inhibits Histone Deacetylase 8 (Hdac8) from the Human Pathogen Schistosoma Mansoni
Authors: Stolfa, D.A. / Marek, M. / Lancelot, J. / Hauser, A.T. / Walter, A. / Leproult, E. / Melesina, J. / Rumpf, T. / Wurtz, J.M. / Cavarelli, J. / Sippl, W. / Pierce, R.J. / Romier, C. / Jung, M.
History
DepositionFeb 14, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: 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)204,92438
Polymers201,7804
Non-polymers3,14534
Water8,125451
1
A: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0157
Polymers50,4451
Non-polymers5706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,27210
Polymers50,4451
Non-polymers8279
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,43812
Polymers50,4451
Non-polymers99311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1999
Polymers50,4451
Non-polymers7548
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.778, 70.815, 98.024
Angle α, β, γ (deg.)77.79, 75.45, 85.40
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, 485 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-9Z8 / 6-(2-Mercaptoacetylamino)-N-phenylhexanamide


Mass: 280.386 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N2O2S
#5: Chemical
ChemComp-DMF / DIMETHYLFORMAMIDE


Mass: 73.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H7NO
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 451 / 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: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 80076 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 33.74 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.2
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.2 / % possible all: 93.8

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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 4BZ6

4bz6


Resolution: 2.3→32.89 Å / Cor.coef. Fo:Fc: 0.9306 / Cor.coef. Fo:Fc free: 0.8976 / SU R Cruickshank DPI: 0.321 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.3 / SU Rfree Blow DPI: 0.213 / SU Rfree Cruickshank DPI: 0.221
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=13636. 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=13636. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=12.
RfactorNum. reflection% reflectionSelection details
Rfree0.2323 4044 5.07 %RANDOM
Rwork0.19 ---
obs0.1922 79759 99.76 %-
Displacement parametersBiso mean: 26.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.8676 Å2-0.7132 Å2-0.5091 Å2
2---1.8136 Å21.0778 Å2
3---0.9459 Å2
Refine analyzeLuzzati coordinate error obs: 0.298 Å
Refinement stepCycle: LAST / Resolution: 2.3→32.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13004 0 185 451 13640
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113529HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0218353HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4486SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes291HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1972HARMONIC5
X-RAY DIFFRACTIONt_it13529HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion17.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1676SEMIHARMONIC5
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_contact16419SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2201 277 4.64 %
Rwork0.1911 5694 -
all0.1926 5971 -
obs--99.76 %
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)
11.01720.012-0.02260.4799-0.32240.84310.0226-0.1532-0.05860.0716-0.0165-0.03090.03570.0348-0.0061-0.08060.0004-0.0132-0.05790.005-0.079153.735425.28985.7706
20.7328-0.07440.0210.3784-0.0950.51520.0151-0.01530.03890.0037-0.02890.0084-0.0376-0.01290.0138-0.0602-0.0021-0.0084-0.06250.0045-0.045188.709343.342470.2401
30.3730.0099-0.15660.9470.04940.5197-0.0240.0094-0.0135-0.07120.01790.0479-0.021-0.0290.0061-0.0322-0.004-0.0114-0.09560.0107-0.060844.23942.36841.2066
40.62370.1382-0.29920.77850.1620.8391-0.07190.1049-0.0891-0.09690.047-0.05220.01710.03680.0249-0.039-0.01240.0095-0.0953-0.0049-0.070665.091235.666625.4888
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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