[English] 日本語
Yorodumi
- PDB-6j3h: Crystal structure of the glutathione S-transferase, CsGST83044, o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6j3h
TitleCrystal structure of the glutathione S-transferase, CsGST83044, of Ceriporiopsis subvermispora in complex with glutathione
ComponentsGlutathione S-transferase
KeywordsTRANSFERASE / glutathione S-transferase / Ceriporiopsis subvermispora
Function / homology
Function and homology information


: / 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 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin ...: / 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 / 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 / GST N-terminal domain-containing protein
Similarity search - Component
Biological speciesCeriporiopsis subvermispora (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsOsman, W.H.W. / Mikami, B. / Saka, N. / Kondo, K. / Nagata, T. / Katahira, M.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science18H04550 Japan
Japan Society for the Promotion of Science18K19397 Japan
Japan Society for the Promotion of Science17K07307 Japan
Japan Society for the Promotion of Science17H05878 Japan
CitationJournal: Int.J.Biol.Macromol. / Year: 2019
Title: Identification of key residues for activities of atypical glutathione S-transferase of Ceriporiopsis subvermispora, a selective degrader of lignin in woody biomass, by crystallography and functional mutagenesis.
Authors: Osman, W.H.W. / Mikami, B. / Saka, N. / Kondo, K. / Lin, M.I. / Nagata, T. / Katahira, M.
History
DepositionJan 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
B: Glutathione S-transferase
C: Glutathione S-transferase
D: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,7888
Polymers121,5584
Non-polymers1,2294
Water2,900161
1
A: Glutathione S-transferase
B: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3944
Polymers60,7792
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-23 kcal/mol
Surface area23720 Å2
MethodPISA
2
C: Glutathione S-transferase
D: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3944
Polymers60,7792
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-23 kcal/mol
Surface area22860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)225.684, 48.397, 150.553
Angle α, β, γ (deg.)90.00, 129.27, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Glutathione S-transferase


Mass: 30389.557 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ceriporiopsis subvermispora (strain B) (fungus)
Gene: CERSUDRAFT_83044 / Production host: Escherichia coli (E. coli) / References: UniProt: M2QJS8
#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.67 Å3/Da / Density % sol: 53.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 8000, 0.1M HEPES-HCl (pH7.5), 0.2M ammonium sulfate, 20% (v/v) 2-propanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 60962 / % possible obs: 93.7 % / Redundancy: 5.9 % / Net I/σ(I): 22.6
Reflection shellResolution: 2.19→2.24 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data collection
MOLREPphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4f03

4f03


Resolution: 2.19→48.763 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.45
RfactorNum. reflection% reflection
Rfree0.259 3107 5.11 %
Rwork0.1998 --
obs0.2028 60850 93.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.19→48.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8433 0 80 161 8674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078790
X-RAY DIFFRACTIONf_angle_d0.88911962
X-RAY DIFFRACTIONf_dihedral_angle_d18.0535164
X-RAY DIFFRACTIONf_chiral_restr0.0531230
X-RAY DIFFRACTIONf_plane_restr0.0061550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1934-2.22770.27531590.242408X-RAY DIFFRACTION88
2.2277-2.26420.33121430.2432666X-RAY DIFFRACTION96
2.2642-2.30330.31431320.23232652X-RAY DIFFRACTION94
2.3033-2.34520.31321420.21792632X-RAY DIFFRACTION96
2.3452-2.39030.28221540.20772670X-RAY DIFFRACTION96
2.3903-2.4390.27691230.21422657X-RAY DIFFRACTION94
2.439-2.49210.2651310.22062645X-RAY DIFFRACTION95
2.4921-2.550.33481380.23042669X-RAY DIFFRACTION94
2.55-2.61380.31971610.22542638X-RAY DIFFRACTION96
2.6138-2.68450.28461440.21852643X-RAY DIFFRACTION93
2.6845-2.76350.3381480.22242597X-RAY DIFFRACTION95
2.7635-2.85270.28941630.22192591X-RAY DIFFRACTION92
2.8527-2.95460.3041270.24092645X-RAY DIFFRACTION94
2.9546-3.07290.28641290.23872604X-RAY DIFFRACTION92
3.0729-3.21270.3111500.23562593X-RAY DIFFRACTION92
3.2127-3.3820.28771360.22752598X-RAY DIFFRACTION92
3.382-3.59390.27441230.21922568X-RAY DIFFRACTION91
3.5939-3.87130.25761460.19282535X-RAY DIFFRACTION90
3.8713-4.26060.20751580.16952502X-RAY DIFFRACTION89
4.2606-4.87670.18191290.15152541X-RAY DIFFRACTION89
4.8767-6.14220.18981470.15952715X-RAY DIFFRACTION94
6.1422-48.77550.19771240.14932974X-RAY DIFFRACTION99

+
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