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- PDB-4l5o: Crystal structure of 26 kDa GST D26H mutant of Clonorchis sinensis -

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Basic information

Entry
Database: PDB / ID: 4l5o
TitleCrystal structure of 26 kDa GST D26H mutant of Clonorchis sinensis
ComponentsPutative glutathione transferaseGlutathione S-transferase
KeywordsTRANSFERASE / GSH binding
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process / metal ion binding
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal ...Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / glutathione transferase
Similarity search - Component
Biological speciesClonorchis sinensis (oriental liver fluke)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å
AuthorsChung, Y.J. / Han, Y.H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Crystal structures of 26kDa Clonorchis sinensis glutathione S-transferase reveal zinc binding and putative metal binding.
Authors: Han, Y.H. / Hong, S.J. / Cheong, H.K. / Chung, Y.J.
History
DepositionJun 11, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Putative glutathione transferase
B: Putative glutathione transferase
C: Putative glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,89514
Polymers75,2663
Non-polymers1,62911
Water4,594255
1
A: Putative glutathione transferase
B: Putative glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1158
Polymers50,1772
Non-polymers9386
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-44 kcal/mol
Surface area19480 Å2
MethodPISA
2
C: Putative glutathione transferase
hetero molecules

C: Putative glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,56012
Polymers50,1772
Non-polymers1,38310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area4820 Å2
ΔGint-98 kcal/mol
Surface area20230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.370, 98.370, 178.501
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe one biological dimer and one monomer are in asymmetric unit. The biological assembly of the monomer is generated by the three fold axis : -x, -x+y, -z+1/3

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Components

#1: Protein Putative glutathione transferase / Glutathione S-transferase


Mass: 25088.648 Da / Num. of mol.: 3 / Mutation: D26H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clonorchis sinensis (oriental liver fluke)
Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q25595
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 3.31 Å3/Da / Density % sol: 62.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris pH8.5, 5mM Zinc sulfate, 2.0M Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.089→85.191 Å / Num. all: 60028 / Num. obs: 60028 / % possible obs: 100 % / Redundancy: 5.9 % / Rsym value: 0.193 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.09-2.25.70.0190.41.928199.9
2.2-2.345.80.0190.61.2931100
2.34-2.55.90.0190.90.891100
2.5-2.760.0191.20.6231100
2.7-2.9560.01920.3781100
2.95-3.360.0193.70.2031100
3.3-3.815.90.0197.10.1031100
3.81-4.675.80.0198.10.0781100
4.67-6.615.50.0199.70.063199.9
6.61-59.55.70.01919.80.029199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.7 Å59.5 Å
Translation2.7 Å59.5 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→59.57 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 5.623 / SU ML: 0.141 / SU R Cruickshank DPI: 0.1738 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24818 3029 5.1 %RANDOM
Rwork0.20171 ---
obs0.20409 56931 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.257 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.26 Å20 Å2
2--0.26 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.09→59.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5286 0 92 255 5633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195538
X-RAY DIFFRACTIONr_bond_other_d0.0010.025129
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.9667518
X-RAY DIFFRACTIONr_angle_other_deg0.8433.00211752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0115650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18423.582268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.79315892
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6711533
X-RAY DIFFRACTIONr_chiral_restr0.1010.2775
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216251
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021344
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.089→2.143 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 236 -
Rwork0.342 4125 -
obs--99.54 %

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