[English] 日本語
Yorodumi
- PDB-5ecs: Crystal Structure of FIP1 with GSH -

+
Open data


ID or keywords:

Loading...

-
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 / response to gravity / glutathione binding / apoplast / glutathione transferase / glutathione transferase activity / glutathione metabolic process / chloroplast / enzyme binding ...regulation of response to red or far red light / toxin catabolic process / response to gravity / glutathione binding / apoplast / 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 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-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 / 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 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more