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- PDB-4gst: REACTION COORDINATE MOTION IN AN SNAR REACTION CATALYZED BY GLUTA... -

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Basic information

Entry
Database: PDB / ID: 4gst
TitleREACTION COORDINATE MOTION IN AN SNAR REACTION CATALYZED BY GLUTATHIONE TRANSFERASE
ComponentsGLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE / GLUTATHIONE TRANSFERASE
Function / homology
Function and homology information


sensory perception of smell / response to metal ion / xenobiotic catabolic process / glutathione binding / nickel cation binding / glutathione transferase / response to lithium ion / response to axon injury / glutathione transferase activity / response to amino acid ...sensory perception of smell / response to metal ion / xenobiotic catabolic process / glutathione binding / nickel cation binding / glutathione transferase / response to lithium ion / response to axon injury / glutathione transferase activity / response to amino acid / glutathione metabolic process / steroid binding / response to lead ion / response to ethanol / response to drug / response to antibiotic / protein kinase binding / protein homodimerization activity / protein-containing complex / extracellular region / cytosol
Glutathione S-transferase, Mu class / Thioredoxin-like superfamily / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal-like / Glutathione S-transferase, C-terminal domain superfamily / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Soluble glutathione S-transferase N-terminal domain profile. / Soluble glutathione S-transferase C-terminal domain profile.
Glutathione S-transferase Mu 1
Biological speciesRattus rattus (black rat)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsJi, X. / Armstrong, R.N. / Gilliland, G.L.
Citation
Journal: Biochemistry / Year: 1993
Title: Snapshots along the reaction coordinate of an SNAr reaction catalyzed by glutathione transferase.
Authors: Ji, X. / Armstrong, R.N. / Gilliland, G.L.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: Tyrosine 115 Participates Both in Chemical and Physical Steps of the Catalytic Mechanism of a Glutathione S-Transferase
Authors: Johnson, W.W. / Liu, S. / Ji, X. / Gilliland, G.L. / Armstrong, R.N.
#2: Journal: J.Biol.Chem. / Year: 1992
Title: Contribution of Tyrosine 6 to the Catalytic Mechanism of Isoenzyme 3-3 of Glutathione S-Transferase
Authors: Liu, S. / Zhang, P. / Ji, X. / Johnson, W.W. / Gilliland, G.L. / Armstrong, R.N.
#3: Journal: Biochemistry / Year: 1992
Title: The Three-Dimensional Structure of a Glutathione S-Transferase from the Mu Gene Class. Structural Analysis of the Binary Complex of Isoenzyme 3-3 and Glutathione at 2.2 Angstroms Resolution
Authors: Ji, X. / Zhang, P. / Armstrong, R.N. / Gilliland, G.L.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 20, 1993 / Release: Oct 31, 1993
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 31, 1993Structure modelrepositoryInitial release
1.1Mar 25, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Nov 29, 2017Structure modelDerived calculations / Otherpdbx_database_status / struct_conf / struct_conf_type_pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE
B: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,25510
Polymers51,6382
Non-polymers1,6178
Water6,485360
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-85 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)88.240, 69.440, 81.280
Angle α, β, γ (deg.)90.00, 106.01, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: RESIDUES 38, 60, AND 206 OF BOTH CHAINS ARE CIS PROLINES.
Components on special symmetry positions
IDModelComponents
11A-426-

HOH

21B-370-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.8258, -0.0683, 0.5599), (-0.0677, -0.9975, -0.0218), (0.5599, -0.0199, -0.8283)
Vector: -6.8929, 31.1531, 26.563)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*, WHICH CORRESPONDS TO A ROTATION OF 179.749 DEGREES AROUND THE DIRECTION 0.9536 -0.0553 0.2959.

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Components

#1: Protein/peptide GLUTATHIONE S-TRANSFERASE /


Mass: 25818.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus rattus (black rat) / References: UniProt: P04905, glutathione transferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Sulfate
#3: Chemical ChemComp-GTD / 1-(S-GLUTATHIONYL)-2,4,6-TRINITROCYCLOHEXA-2,5-DIENE / (S)-2-AMINO-5-((R)-1-(CARBOXYMETHYLAMINO)-1-OXO-3-(2,4,6-TRINITROCYCLOHEXA-2,5-DIENYLTHIO)PROPAN-2-YLAMINO)-5-OXOPENTANOIC ACID


Mass: 520.428 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20N6O12S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.9 / Method: vapor diffusion, hanging drop
Details: referred to 'Sesay, M. A.', (1987) J.Mol.Biol., 197, 377-378
Components of the solutions
*PLUS

Crystal-ID: 1

IDConc.Common nameSol-IDChemical formula
111.3 mg/mlproteindrop
23.5 mM(9R,-10R)-9,10-dihydro-9-(S-glutathionyl)-10-hydroxyphenanthrenedrop
30.4 %(w/v)beta-octylglucopyranosidedrop
440 %(w/v)satammonium sulfatedrop
510 mMdropKH2PO4
660-74 %(w/v)satammonium sulfatereservoir
70.46 %(w/v)beta-octylglucopyranosidereservoir
810 mMreservoirKH2PO4

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Data collection

Reflection
*PLUS
Highest resolution: 1.9 Å / Num. all: 91596 / Num. obs: 36138 / Rmerge(I) obs: 0.0657

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Processing

SoftwareName: GPRLSA / Classification: refinement
RefinementRfactor obs: 0.18 / Highest resolution: 1.9 Å
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3636 0 100 360 4096
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 6 Å / Num. reflection obs: 29072 / σ(I): 2 / Rfactor obs: 0.18
Refine LS restraints
*PLUS
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_planar_d0.036
X-RAY DIFFRACTIONp_chiral_restr0.211
X-RAY DIFFRACTIONp_mcbond_it0.812
X-RAY DIFFRACTIONp_scbond_it1.32
X-RAY DIFFRACTIONp_mcangle_it1.367
X-RAY DIFFRACTIONp_scangle_it2.002

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