[English] 日本語
Yorodumi
- PDB-5g5a: Glutathione transferase U25 from Arabidopsis thaliana in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5g5a
TitleGlutathione transferase U25 from Arabidopsis thaliana in complex with glutathione disulfide
ComponentsGLUTATHIONE S-TRANSFERASE U25
KeywordsTRANSFERASE / GLUTATHIONE / ARABIDOPSIS / TNT
Function / homology
Function and homology information


2,4,6-trinitrotoluene catabolic process / toxin catabolic process / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytosol / cytoplasm
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 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-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 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 U25
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsAhmad, L. / Rylott, E. / Bruce, N.C. / Grogan, G.
CitationJournal: To be Published
Title: Structure of Glutathione Transferase U25 from Arabidopsis Thaliana
Authors: Ahmad, L. / Rylott, E. / Bruce, N.C. / Grogan, G.
History
DepositionMay 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE U25
B: GLUTATHIONE S-TRANSFERASE U25
C: GLUTATHIONE S-TRANSFERASE U25
D: GLUTATHIONE S-TRANSFERASE U25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,95312
Polymers102,4944
Non-polymers2,4598
Water12,953719
1
A: GLUTATHIONE S-TRANSFERASE U25
B: GLUTATHIONE S-TRANSFERASE U25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4766
Polymers51,2472
Non-polymers1,2294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-34.7 kcal/mol
Surface area18300 Å2
MethodPISA
2
C: GLUTATHIONE S-TRANSFERASE U25
D: GLUTATHIONE S-TRANSFERASE U25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4766
Polymers51,2472
Non-polymers1,2294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-37.7 kcal/mol
Surface area18200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.830, 107.668, 108.755
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9433, 0.3184, -0.0934), (0.3144, 0.7677, -0.5584), (-0.1061, -0.5561, -0.8243)-26.08, 1.901, -9.121
2given(0.9106, -0.3118, -0.2713), (-0.4118, -0.7399, -0.532), (-0.03485, 0.5961, -0.8021)10.61, 14.64, -25.73
3given(-0.9881, -0.05407, 0.1439), (0.04371, -0.9963, -0.07418), (0.1474, -0.06701, 0.9868)-27.19, 31.43, 3.415

-
Components

#1: Protein
GLUTATHIONE S-TRANSFERASE U25


Mass: 25623.514 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): TUNER / References: UniProt: Q9SHH7, glutathione transferase
#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 719 / 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: 2.52 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 5.5
Details: 0.2 M AMMONIUM ACETATE, 0.1 M BIS-TRIS PROPANE PH 5.5 AND 23 % (W/V) PEG 3350; 2 MM GSH

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.95→48.54 Å / Num. obs: 75638 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.7
Reflection shellResolution: 1.95→1.99 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4TOP

4top


Resolution: 1.95→48.54 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.465 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21736 3688 4.9 %RANDOM
Rwork0.20458 ---
obs0.20521 71875 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.894 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--16.35 Å20 Å2
3----16.2 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7045 0 160 719 7924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0197407
X-RAY DIFFRACTIONr_bond_other_d0.0140.026977
X-RAY DIFFRACTIONr_angle_refined_deg1.9351.97910008
X-RAY DIFFRACTIONr_angle_other_deg1.814316127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.555873
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94824.198324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71151261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9281532
X-RAY DIFFRACTIONr_chiral_restr0.1220.21056
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0218204
X-RAY DIFFRACTIONr_gen_planes_other0.010.021676
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1973.0433498
X-RAY DIFFRACTIONr_mcbond_other3.1953.0423497
X-RAY DIFFRACTIONr_mcangle_it3.7414.554366
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.3213.4013909
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 284 -
Rwork0.413 5228 -
obs--99.78 %

+
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://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