[English] 日本語
Yorodumi
- PDB-3wd6: Crystal structure of Bombyx mori omega-class glutathione transfer... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wd6
TitleCrystal structure of Bombyx mori omega-class glutathione transferase in complex with GSH
ComponentsOmega-class glutathione S-transferase
KeywordsTRANSFERASE / electron sharing network / glutathione binding
Function / homology
Function and homology information


glutathione transferase activity / oxidoreductase activity / cytoplasm
Similarity search - Function
Glutathione S-transferase, omega-class / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-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, omega-class / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-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 / IODIDE ION / : / DI(HYDROXYETHYL)ETHER / Omega-class glutathione S-transferase
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYamamoto, K. / Suzuki, M. / Higashiura, A. / Nakagawa, A.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Three-dimensional structure of a Bombyx mori Omega-class glutathione transferase.
Authors: Yamamoto, K. / Suzuki, M. / Higashiura, A. / Nakagawa, A.
History
DepositionJun 7, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Omega-class glutathione S-transferase
B: Omega-class glutathione S-transferase
C: Omega-class glutathione S-transferase
D: Omega-class glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,60224
Polymers119,3904
Non-polymers2,21220
Water5,963331
1
A: Omega-class glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4407
Polymers29,8471
Non-polymers5936
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Omega-class glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2955
Polymers29,8471
Non-polymers4484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Omega-class glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4847
Polymers29,8471
Non-polymers6376
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Omega-class glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3835
Polymers29,8471
Non-polymers5354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Omega-class glutathione S-transferase
hetero molecules

D: Omega-class glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,82312
Polymers59,6952
Non-polymers1,12810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area5130 Å2
ΔGint-25 kcal/mol
Surface area21400 Å2
MethodPISA
6
B: Omega-class glutathione S-transferase
C: Omega-class glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,77912
Polymers59,6952
Non-polymers1,08410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-27 kcal/mol
Surface area21120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.861, 89.894, 182.149
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Omega-class glutathione S-transferase / Uncharacterized protein


Mass: 29847.375 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: gsto, GSTo2 / Production host: Escherichia coli (E. coli) / References: UniProt: A8R5V3

-
Non-polymers , 6 types, 351 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#6: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.6 Å3/Da / Density % sol: 52.71 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M potassium iodide, and 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorDetector: CCD
RadiationMonochromator: DXM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→32.84 Å / Num. obs: 43880 / % possible obs: 98.4 %
Reflection shellResolution: 2.5→2.64 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MERLOTphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→32.84 Å / SU ML: 0.76 / σ(F): 0.97 / Phase error: 26.1 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2564 2185 5.01 %
Rwork0.2079 --
obs0.2104 43880 99.83 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.25 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.2984 Å20 Å2-0 Å2
2--2.3362 Å20 Å2
3----3.6345 Å2
Refinement stepCycle: LAST / Resolution: 2.5→32.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7968 0 117 331 8416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098270
X-RAY DIFFRACTIONf_angle_d1.08811213
X-RAY DIFFRACTIONf_dihedral_angle_d16.8663135
X-RAY DIFFRACTIONf_chiral_restr0.0721234
X-RAY DIFFRACTIONf_plane_restr0.0051432
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4999-2.52830.2581290.2447251797
2.5283-2.55810.35381230.252657100
2.5581-2.58930.29661460.26032606100
2.5893-2.6220.32691350.25132650100
2.622-2.65650.321370.26142601100
2.6565-2.69290.29461370.25272654100
2.6929-2.73130.33241530.24092624100
2.7313-2.77210.33281340.25442607100
2.7721-2.81540.33591580.24022719100
2.8154-2.86150.28481220.24792567100
2.8615-2.91080.33791430.23042670100
2.9108-2.96370.29481290.22582632100
2.9637-3.02070.2951330.2262672100
3.0207-3.08230.26731530.22412606100
3.0823-3.14930.27081290.22272647100
3.1493-3.22250.28721600.2172587100
3.2225-3.3030.25971500.20762640100
3.303-3.39220.25181410.21152644100
3.3922-3.49190.24461510.2022599100
3.4919-3.60450.24331510.20582655100
3.6045-3.73310.26981300.20942608100
3.7331-3.88240.24061280.19032653100
3.8824-4.05880.2451240.1772669100
4.0588-4.27230.21691460.16332618100
4.2723-4.53940.21171290.17562652100
4.5394-4.88880.21261130.16662655100
4.8888-5.37890.22431410.18292640100
5.3789-6.15280.25751440.21832620100
6.1528-7.73510.22281470.21742628100
7.7351-32.84230.19951440.1944259598

+
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