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- PDB-4bz5: Crystal structure of Schistosoma mansoni HDAC8 -

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Basic information

Entry
Database: PDB / ID: 4bz5
TitleCrystal structure of Schistosoma mansoni HDAC8
ComponentsHISTONE DEACETYLASE 8
KeywordsHYDROLASE / PLATYHELMINTHS / 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
: / L(+)-TARTARIC ACID / histone deacetylase
Similarity search - Component
Biological speciesSCHISTOSOMA MANSONI (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.785 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)202,95420
Polymers201,7804
Non-polymers1,17516
Water27,5991532
1
A: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7395
Polymers50,4451
Non-polymers2944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7395
Polymers50,4451
Non-polymers2944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7395
Polymers50,4451
Non-polymers2944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7395
Polymers50,4451
Non-polymers2944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.649, 70.734, 98.295
Angle α, β, γ (deg.)75.90, 78.32, 85.59
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-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1532 / 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: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 166229 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Biso Wilson estimate: 17.94 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 26.5
Reflection shellResolution: 1.79→1.82 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 5 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T67

1t67


Resolution: 1.785→31.37 Å / SU ML: 0.4 / σ(F): 1.98 / Phase error: 18.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1883 8324 5 %
Rwork0.1544 --
obs0.1561 166214 96.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.43 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 23.68 Å2
Baniso -1Baniso -2Baniso -3
1-2.0077 Å21.336 Å2-0.4346 Å2
2--1.4564 Å2-0.0831 Å2
3----3.4641 Å2
Refinement stepCycle: LAST / Resolution: 1.785→31.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13152 0 52 1532 14736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513631
X-RAY DIFFRACTIONf_angle_d0.88118566
X-RAY DIFFRACTIONf_dihedral_angle_d11.6784905
X-RAY DIFFRACTIONf_chiral_restr0.0642011
X-RAY DIFFRACTIONf_plane_restr0.0042386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7852-1.80550.23052360.19124418X-RAY DIFFRACTION81
1.8055-1.82670.2632540.19485210X-RAY DIFFRACTION97
1.8267-1.8490.23052590.17665379X-RAY DIFFRACTION97
1.849-1.87240.2192860.16915202X-RAY DIFFRACTION97
1.8724-1.8970.222820.17025286X-RAY DIFFRACTION97
1.897-1.9230.21112890.16175290X-RAY DIFFRACTION97
1.923-1.95050.20172760.15475249X-RAY DIFFRACTION97
1.9505-1.97960.19162550.15485297X-RAY DIFFRACTION97
1.9796-2.01050.20742830.15825348X-RAY DIFFRACTION97
2.0105-2.04350.20742740.15215284X-RAY DIFFRACTION97
2.0435-2.07870.19052460.15985338X-RAY DIFFRACTION98
2.0787-2.11650.22762560.14955302X-RAY DIFFRACTION98
2.1165-2.15720.17832740.15065274X-RAY DIFFRACTION97
2.1572-2.20120.18323140.14765296X-RAY DIFFRACTION98
2.2012-2.24910.19422880.14555265X-RAY DIFFRACTION98
2.2491-2.30140.16612800.14545329X-RAY DIFFRACTION98
2.3014-2.35890.17752840.14715358X-RAY DIFFRACTION98
2.3589-2.42270.18192760.15235251X-RAY DIFFRACTION98
2.4227-2.49390.20322860.15675278X-RAY DIFFRACTION98
2.4939-2.57440.20023150.16265302X-RAY DIFFRACTION98
2.5744-2.66640.18983020.15955329X-RAY DIFFRACTION98
2.6664-2.77310.19592870.15855282X-RAY DIFFRACTION98
2.7731-2.89920.20452810.1585324X-RAY DIFFRACTION98
2.8992-3.05190.20872580.16465349X-RAY DIFFRACTION98
3.0519-3.24290.18932720.16185342X-RAY DIFFRACTION98
3.2429-3.4930.17072740.15235329X-RAY DIFFRACTION98
3.493-3.8440.18792900.14885346X-RAY DIFFRACTION98
3.844-4.39890.15242770.12775374X-RAY DIFFRACTION98
4.3989-5.53720.15712850.13495329X-RAY DIFFRACTION99
5.5372-31.37490.18712850.18394930X-RAY DIFFRACTION91
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)
10.83750.0407-0.10620.3781-0.17790.55150.0054-0.0848-0.08030.0391-0.0003-0.01560.02660.01720.00050.0658-0.0097-0.00990.10540.0090.085653.143724.733485.4884
20.6183-0.17840.1570.2948-0.10280.40920.007-0.06380.0186-0.0033-0.0190.0002-0.0229-0.0252-0.01780.0370.00420.00850.0987-0.00240.070188.180143.080170.7686
30.2725-0.142-0.12390.61480.13070.4633-0.01420.00670.0017-0.0216-0.00260.0489-0.0297-0.0305-0.01270.0731-0.001-0.01270.03880.00030.070944.56712.813640.3907
40.34870.0895-0.13560.8187-0.28530.5374-0.02210.0191-0.008-0.1548-0.0011-0.05180.10630.0146-0.00690.1558-0.01080.00790.0499-0.01320.071765.426636.458725.6011
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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