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- PDB-2wb9: Fasciola hepatica sigma class GST -

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Basic information

Entry
Database: PDB / ID: 2wb9
TitleFasciola hepatica sigma class GST
ComponentsGLUTATHIONE TRANSFERASE SIGMA CLASS
KeywordsTRANSFERASE / THIOREDOXIN FOLD
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process
Similarity search - Function
Glutathione S-transferase, C-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 ...Glutathione S-transferase, C-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
BROMIDE ION / CYSTEINE / GLUTATHIONE / glutathione transferase
Similarity search - Component
Biological speciesFASCIOLA HEPATICA (liver fluke)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsLine, K. / Isupov, M.N. / LaCourse, J. / Brophy, P.M. / Littlechild, J.A.
CitationJournal: To be Published
Title: The 1.6 Angstrom Crystal Structure of the Fasciola Hepatica Sigma Class Gst
Authors: Line, K. / Isupov, M.N. / Lacourse, J. / Brophy, P.M. / Littlechild, J.A.
History
DepositionFeb 23, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Dec 13, 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 / 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 / _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: GLUTATHIONE TRANSFERASE SIGMA CLASS
B: GLUTATHIONE TRANSFERASE SIGMA CLASS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,27810
Polymers49,1432
Non-polymers1,1358
Water8,935496
1
A: GLUTATHIONE TRANSFERASE SIGMA CLASS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2406
Polymers24,5711
Non-polymers6685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GLUTATHIONE TRANSFERASE SIGMA CLASS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0394
Polymers24,5711
Non-polymers4673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.728, 87.751, 93.781
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GLUTATHIONE TRANSFERASE SIGMA CLASS / GLUTATHIONE TRANSFERASE


Mass: 24571.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) FASCIOLA HEPATICA (liver fluke) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q06A71, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-CYS / CYSTEINE / Cysteine


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#4: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 496 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsGLUTATHIONE (GSH): SUBUNIT B IS GLUTATHIONE ALONE, SUBUNIT A GLUTATHIONE IS COVALENTLY BOUND TO CYSTEINE (CGL)

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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: 2.38 Å3/Da / Density % sol: 48.32 % / Description: NONE
Crystal growDetails: 0.15M KBR, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS ROTATING ANODE GENERATOR / Wavelength: 1.514
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 21, 2009 / Details: XENOCS FOX2D CU_25P
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 1.59→19.43 Å / Num. obs: 62227 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.8
Reflection shellResolution: 1.59→1.68 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.4 / % possible all: 91.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U3I

1u3i


Resolution: 1.59→64.02 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.007 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22243 1899 3.1 %RANDOM
Rwork0.17517 ---
obs0.17661 60197 97.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.171 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.59→64.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3442 0 52 496 3990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0223853
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.411.9985254
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5585503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.81223.149181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.62115748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5771533
X-RAY DIFFRACTIONr_chiral_restr0.1980.2566
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022965
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.22012
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3270.22659
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2457
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.250
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.542314
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.62563666
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.781769
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.737101541
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: 1.592→1.633 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.486 125 -
Rwork0.405 3827 -
obs--85.25 %

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