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- PDB-1n2a: Crystal Structure of a Bacterial Glutathione Transferase from Esc... -

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Basic information

Entry
Database: PDB / ID: 1n2a
TitleCrystal Structure of a Bacterial Glutathione Transferase from Escherichia coli with Glutathione Sulfonate in the Active Site
ComponentsGlutathione S-transferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / response to hydrogen peroxide / protein homodimerization activity / cytoplasm
Similarity search - Function
Glutathione S-transferase, N-terminal domain / 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 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. ...Glutathione S-transferase, N-terminal domain / 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 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-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 SULFONIC ACID / Glutathione S-transferase GstA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRife, C.L. / Parsons, J.F. / Xiao, G. / Gilliland, G.L. / Armstrong, R.N.
CitationJournal: Proteins / Year: 2003
Title: Conserved structural elements in glutathione transferase homologues encoded in the genome of Escherichia coli
Authors: Rife, C.L. / Parsons, J.F. / Xiao, G. / Gilliland, G.L. / Armstrong, R.N.
History
DepositionOct 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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_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
B: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5034
Polymers45,7932
Non-polymers7112
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-14 kcal/mol
Surface area16510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.616, 57.166, 134.927
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer composed of chains A and B.

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Components

#1: Protein Glutathione S-transferase


Mass: 22896.342 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GT_1787923 / Plasmid: PET20 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) / References: UniProt: P0A9D2, glutathione transferase
#2: Chemical ChemComp-GTS / GLUTATHIONE SULFONIC ACID


Mass: 355.322 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O9S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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 Å3/Da / Density % sol: 38.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: PEG 3000, B-n-octyl-glucopyranoside, glutathione sulfonate, sodium acetate, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-20 mg/mlprotein1drop
23-5 mMglutathione sulfonate1drop
30.3 %beta-n-octylglucopyranoside1drop
47 %PEG30001drop
50.1 Msodium acetate1reservoir
614-18 %PEG30001reservoirpH4.7

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 10, 1997
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→19.7 Å / Num. obs: 23318 / % possible obs: 87.53 % / Observed criterion σ(F): 4 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.042
Reflection
*PLUS
% possible obs: 86.8 % / Redundancy: 11 % / Rmerge(I) obs: 0.041
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.97 Å / % possible obs: 41.6 % / Rmerge(I) obs: 0.22

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AOF

1aof


Resolution: 1.9→19.17 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.901 / SU B: 4.128 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 4 / ESU R: 0.229 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26005 2563 9.9 %RANDOM
Rwork0.19452 ---
all0.234 ---
obs0.20089 23318 87.53 %-
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: 28.321 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3107 0 46 153 3306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223220
X-RAY DIFFRACTIONr_bond_other_d0.0020.022961
X-RAY DIFFRACTIONr_angle_refined_deg1.8581.9854364
X-RAY DIFFRACTIONr_angle_other_deg1.05636900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.245384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1410.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023485
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02640
X-RAY DIFFRACTIONr_nbd_refined0.2230.2740
X-RAY DIFFRACTIONr_nbd_other0.2350.23234
X-RAY DIFFRACTIONr_nbtor_other0.0880.21682
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2138
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3430.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.1641.51939
X-RAY DIFFRACTIONr_mcangle_it2.08123121
X-RAY DIFFRACTIONr_scbond_it2.89431281
X-RAY DIFFRACTIONr_scangle_it4.7594.51243
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.953 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 88 -
Rwork0.211 807 -
obs--87.4 %
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 19.7 Å / Num. reflection obs: 21775 / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.86

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