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- PDB-3iso: Crystal structure of 26 kDa GST of Clonorchis sinensis in P3221 s... -

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Basic information

Entry
Database: PDB / ID: 3iso
TitleCrystal structure of 26 kDa GST of Clonorchis sinensis in P3221 symmetry
ComponentsPutative glutathione transferaseGlutathione S-transferase
KeywordsTRANSFERASE / GST
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / 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: 1.9 Å
AuthorsHan, Y.H. / Seo, H.A. / Kim, G.H. / Chung, Y.J.
CitationJournal: Protein Expr.Purif. / Year: 2010
Title: A histidine substitution confers metal binding affinity to a Schistosoma japonicum Glutathione S-transferase.
Authors: Han, Y.H. / Seo, H.A. / Kim, G.H. / Lee, C.K. / Kang, Y.K. / Ryu, K.H. / Chung, Y.J.
History
DepositionAug 27, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,64514
Polymers50,1312
Non-polymers1,51412
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-171 kcal/mol
Surface area19640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.390, 96.390, 115.428
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 25065.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clonorchis sinensis (oriental liver fluke)
Plasmid: pET28 / 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.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 3.1 Å3/Da / Density % sol: 60.28 % / Mosaicity: 0.27 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris pH8.5, 2.0M Ammonium sulfate, 5mM Zinc 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 315 / Detector: CCD / Date: Mar 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→83.48 Å / Num. all: 49367 / Num. obs: 49299 / % possible obs: 99.9 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.058 / Χ2: 2.305 / Net I/σ(I): 20
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.9710.20.1348531.231100
1.97-2.0510.30.1148911.398100
2.05-2.1410.40.09648911.61100
2.14-2.2510.50.08148621.656100
2.25-2.3910.50.07649131.895100
2.39-2.5810.60.07948922.585100
2.58-2.8410.80.09149334.211100
2.84-3.2510.80.08249344.776100
3.25-4.0910.30.04149921.99699.8
4.09-5010.50.03151381.48899.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M9A

1m9a


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.226 / WRfactor Rwork: 0.182 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.877 / SU B: 2.263 / SU ML: 0.069 / SU R Cruickshank DPI: 0.122 / SU Rfree: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2489 5.1 %RANDOM
Rwork0.179 46772 --
obs0.181 49261 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 69.94 Å2 / Biso mean: 18.553 Å2 / Biso min: 2.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.05 Å20 Å2
2--0.11 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3540 0 82 253 3875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0223714
X-RAY DIFFRACTIONr_angle_refined_deg2.1871.9775042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4615434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.26423.708178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74215602
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1831522
X-RAY DIFFRACTIONr_chiral_restr0.3120.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212874
X-RAY DIFFRACTIONr_mcbond_it1.4161.52174
X-RAY DIFFRACTIONr_mcangle_it2.33323498
X-RAY DIFFRACTIONr_scbond_it3.59731540
X-RAY DIFFRACTIONr_scangle_it5.4024.51544
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 173 -
Rwork0.177 3399 -
all-3572 -
obs--99.61 %

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