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- PDB-1ua5: Non-fusion GST from S. japonicum in complex with glutathione -

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Basic information

Entry
Database: PDB / ID: 1ua5
TitleNon-fusion GST from S. japonicum in complex with glutathione
Componentsglutathione S-transferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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 S-transferase class-mu 26 kDa isozyme
Similarity search - Component
Biological speciesSchistosoma japonicum (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKursula, I. / Heape, A.M. / Kursula, P.
CitationJournal: Protein Pept.Lett. / Year: 2005
Title: Crystal structure of non-fused glutathione S-transferase from Schistosoma japonicum in complex with glutathione.
Authors: Kursula, I. / Heape, A.M. / Kursula, P.
History
DepositionFeb 28, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Dec 7, 2011Group: Non-polymer description
Revision 1.4Dec 4, 2019Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9383
Polymers25,5351
Non-polymers4032
Water2,090116
1
A: glutathione S-transferase
hetero molecules

A: glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8766
Polymers51,0692
Non-polymers8074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4430 Å2
ΔGint-38 kcal/mol
Surface area18990 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.527, 92.527, 57.657
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1042-

HOH

21A-1097-

HOH

31A-1103-

HOH

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Components

#1: Protein glutathione S-transferase / / glutathione S-transferase 26 kDa


Mass: 25534.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma japonicum (invertebrata) / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P08515, glutathione transferase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.31 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: ammonium sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 8868 / Num. obs: 8868 / % possible obs: 97.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 38 Å2 / Rsym value: 0.1 / Net I/σ(I): 10.7
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3 / Num. unique all: 974 / Rsym value: 0.465 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.1.27refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 10.242 / SU ML: 0.217 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.685 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22134 443 5 %RANDOM
Rwork0.16905 ---
all0.17182 8851 --
obs0.17182 8851 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.031 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2--0.86 Å20 Å2
3----1.73 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1770 0 25 116 1911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221841
X-RAY DIFFRACTIONr_bond_other_d0.0020.021660
X-RAY DIFFRACTIONr_angle_refined_deg1.3281.9892484
X-RAY DIFFRACTIONr_angle_other_deg0.79233885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0925214
X-RAY DIFFRACTIONr_chiral_restr0.0720.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021992
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02371
X-RAY DIFFRACTIONr_nbd_refined0.1960.2377
X-RAY DIFFRACTIONr_nbd_other0.2210.21906
X-RAY DIFFRACTIONr_nbtor_other0.0930.21034
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.275
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2280.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2460.28
X-RAY DIFFRACTIONr_mcbond_it1.05831072
X-RAY DIFFRACTIONr_mcangle_it1.78241729
X-RAY DIFFRACTIONr_scbond_it1.0383769
X-RAY DIFFRACTIONr_scangle_it1.6724755
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.411 32
Rwork0.234 600
Refinement TLS params.Method: refined / Origin x: 10.214 Å / Origin y: 74.772 Å / Origin z: 3.411 Å
111213212223313233
T0.0561 Å20.0118 Å2-0.0316 Å2-0.0364 Å20.0168 Å2--0.1001 Å2
L2.2666 °20.4975 °2-0.1177 °2-1.7233 °2-0.1274 °2--2.3035 °2
S-0.0093 Å °0.0695 Å °0.0278 Å °-0.158 Å °-0.0099 Å °0.0391 Å °0.0657 Å °0.0144 Å °0.0193 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2152 - 216
2X-RAY DIFFRACTION1AC10021 - 1002

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