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- PDB-5ecs: Crystal Structure of FIP1 with GSH -

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Basic information

Entry
Database: PDB / ID: 5ecs
TitleCrystal Structure of FIP1 with GSH
ComponentsGlutathione S-transferase U20
KeywordsTRANSFERASE / Glutathione S-transferase
Function / homology
Function and homology information


regulation of response to red or far red light / toxin catabolic process / glutathione binding / apoplast / response to gravity / glutathione transferase / glutathione transferase activity / glutathione metabolic process / chloroplast / enzyme binding ...regulation of response to red or far red light / toxin catabolic process / glutathione binding / apoplast / response to gravity / glutathione transferase / glutathione transferase activity / glutathione metabolic process / chloroplast / enzyme binding / mitochondrion / nucleus / cytoplasm / cytosol
Similarity search - Function
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant / Glutathione S-transferase Omega/Tau-like / 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 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-transferases Tau, C-terminal alpha helical domain, plant / Glutathione S-transferase Omega/Tau-like / 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 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 / Glutathione S-transferase U20
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65000262305 Å
AuthorsChen, C.Y. / Cheng, Y.S.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural basis of jasmonate-amido synthetase FIN219 in complex with glutathione S-transferase FIP1 during the JA signal regulation
Authors: Chen, C.Y. / Ho, S.S. / Kuo, T.Y. / Hsieh, H.L. / Cheng, Y.S.
History
DepositionOct 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Mar 22, 2017Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S-transferase U20
B: Glutathione S-transferase U20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3494
Polymers51,7352
Non-polymers6152
Water4,828268
1
A: Glutathione S-transferase U20
hetero molecules

A: Glutathione S-transferase U20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3494
Polymers51,7352
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area2220 Å2
ΔGint-12 kcal/mol
Surface area18650 Å2
MethodPISA
2
B: Glutathione S-transferase U20
hetero molecules

B: Glutathione S-transferase U20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3494
Polymers51,7352
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2270 Å2
ΔGint-10 kcal/mol
Surface area18780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.383, 58.893, 97.900
Angle α, β, γ (deg.)90.000, 100.500, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11A-424-

HOH

21B-454-

HOH

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Components

#1: Protein Glutathione S-transferase U20 / AtGSTU20 / FIN219-interacting protein 1 / GST class-tau member 20


Mass: 25867.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GSTU20, FIP1, At1g78370, F3F9.11 / Plasmid: pRSET-B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8L7C9, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M sodium acetate trihydrate, 0.1 M Tris-HCl, 30%(w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 60431 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 17.4150366692 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/av σ(I): 21.624 / Net I/σ(I): 13.9
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 4.09 / Rsym value: 0.358 / % possible all: 97.1

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Processing

Software
NameVersionClassification
HKL-2000v708data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.6phasing
PHENIX1.9_1692+svnmodel building
Coot0.8.2model building
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VO4

2vo4


Resolution: 1.65000262305→26.6503929074 Å / SU ML: 0.146807005221 / Cross valid method: FREE R-VALUE / σ(F): 1.34368788552 / Phase error: 18.3123962951
RfactorNum. reflection% reflection
Rfree0.188001140282 1998 3.30625010342 %
Rwork0.170338000192 58433 -
obs0.170927337186 60431 99.1436024478 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.3235357518 Å2
Refinement stepCycle: final / Resolution: 1.65000262305→26.6503929074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3496 0 40 268 3804
Biso mean--24.71 29.87 -
Num. residues----428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00729194666163636
X-RAY DIFFRACTIONf_angle_d1.079464469674904
X-RAY DIFFRACTIONf_chiral_restr0.0459447093442490
X-RAY DIFFRACTIONf_plane_restr0.00543261942688636
X-RAY DIFFRACTIONf_dihedral_angle_d12.25000352561352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.69130.2457012120131400.1949701905744111X-RAY DIFFRACTION98.4711605281
1.6913-1.7370.2047463054851430.1833293758764194X-RAY DIFFRACTION99.3357764544
1.737-1.78810.2164646703271420.1802242023564123X-RAY DIFFRACTION99.6029892574
1.7881-1.84580.2046865725751410.1743704140264136X-RAY DIFFRACTION99.0734306231
1.8458-1.91170.2074058386371420.1703034513234170X-RAY DIFFRACTION99.1948470209
1.9117-1.98830.2181122302511420.1611151637474157X-RAY DIFFRACTION98.9413118527
1.9883-2.07870.1856687861351430.1663364929264159X-RAY DIFFRACTION99.0331491713
2.0787-2.18830.2007172479681420.1710853576064129X-RAY DIFFRACTION98.6601986602
2.1883-2.32530.2004770091731400.1634846153014142X-RAY DIFFRACTION98.66359447
2.3253-2.50470.2057656355891440.1715805870954165X-RAY DIFFRACTION99.3773062731
2.5047-2.75650.1776420954541430.1695927016754208X-RAY DIFFRACTION99.6336157545
2.7565-3.15480.1790188097521460.1781397328354244X-RAY DIFFRACTION99.8862343572
3.1548-3.97270.1704762772771440.1613371642044230X-RAY DIFFRACTION99.8402191281
3.9727-26.65390.1725594883251460.1720475533564265X-RAY DIFFRACTION98.3719892953

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