[English] 日本語
Yorodumi
- PDB-5uuo: Crystal structure of SARO_2595 from Novosphingobium aromaticivorans -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uuo
TitleCrystal structure of SARO_2595 from Novosphingobium aromaticivorans
ComponentsGlutathione S-transferase-like protein
KeywordsTRANSFERASE / Bioenergy / GLBRC / lignin valorization
Function / homology
Function and homology information


transferase activity
Similarity search - Function
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, C-terminal / 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 / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / 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-like protein
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.25 Å
AuthorsBingman, C.A. / Kontur, W.S. / Olmsted, C.N. / Fox, B.G. / Donohue, T.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FC02-07ER64494 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Novosphingobium aromaticivoransuses a Nu-class glutathioneS-transferase as a glutathione lyase in breaking the beta-aryl ether bond of lignin.
Authors: Kontur, W.S. / Bingman, C.A. / Olmsted, C.N. / Wassarman, D.R. / Ulbrich, A. / Gall, D.L. / Smith, R.W. / Yusko, L.M. / Fox, B.G. / Noguera, D.R. / Coon, J.J. / Donohue, T.J.
History
DepositionFeb 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Apr 18, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / pdbx_entity_nonpoly
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.1Mar 16, 2022Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_audit_support / pdbx_entity_nonpoly
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_audit_support.funding_organization / _pdbx_entity_nonpoly.name
Revision 2.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Glutathione S-transferase-like protein
A: Glutathione S-transferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,76228
Polymers65,0312
Non-polymers2,73126
Water13,727762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13490 Å2
ΔGint-53 kcal/mol
Surface area21580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.810, 70.390, 168.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Glutathione S-transferase-like protein


Mass: 32515.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CIP 105152 / NBRC 16084 / F199) (bacteria)
Strain: ATCC 700278 / DSM 12444 / CIP 105152 / NBRC 16084 / F199
Gene: Saro_2595 / Plasmid: pVP302K / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q2G542
#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 762 / 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: 3.09 Å3/Da / Density % sol: 60.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Saro protein at 277 mM was incubated with 10 mM reduced glutathione for 50 minutes prior to setting up crystallization experiments. The droplet yielding the crystal with the highest observed ...Details: Saro protein at 277 mM was incubated with 10 mM reduced glutathione for 50 minutes prior to setting up crystallization experiments. The droplet yielding the crystal with the highest observed diffracting power was composed of 130 nL protein and 85 nL reservoir solution. The reservoir solution was 1.35 M ammonium sulfate, 0.1 M lithium sulfate 0.1 M bis-trispropane, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.7749 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2016
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.25→29.36 Å / Num. obs: 225442 / % possible obs: 99.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 16.03 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05235 / Rpim(I) all: 0.01485 / Net I/σ(I): 21.85
Reflection shellResolution: 1.25→1.28 Å / Redundancy: 13.9 % / Rmerge(I) obs: 1.297 / Mean I/σ(I) obs: 1.96 / Num. unique obs: 16479 / CC1/2: 0.841 / Rpim(I) all: 0.3565 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XSCALEMay 1, 2016 BUILT=20160617data reduction
XDSVERSION Oct 15, 2015data scaling
PHASER2.6.0phasing
RefinementResolution: 1.25→29.81 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1323 1963 0.87 %thin shells
Rwork0.1303 ---
obs0.1303 225263 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4497 0 172 762 5431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075004
X-RAY DIFFRACTIONf_angle_d1.0246764
X-RAY DIFFRACTIONf_dihedral_angle_d14.3911782
X-RAY DIFFRACTIONf_chiral_restr0.077670
X-RAY DIFFRACTIONf_plane_restr0.007901
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.28130.31451430.268915731X-RAY DIFFRACTION100
1.2813-1.31590.25491330.230615754X-RAY DIFFRACTION100
1.3159-1.35460.20761320.196515845X-RAY DIFFRACTION100
1.3546-1.39840.16711500.174915772X-RAY DIFFRACTION100
1.3984-1.44830.16821270.157115850X-RAY DIFFRACTION100
1.4483-1.50630.12671560.13915843X-RAY DIFFRACTION100
1.5063-1.57490.13171290.124215894X-RAY DIFFRACTION100
1.5749-1.65790.12841310.117615876X-RAY DIFFRACTION100
1.6579-1.76180.11611690.117615951X-RAY DIFFRACTION100
1.7618-1.89780.1103990.117115953X-RAY DIFFRACTION100
1.8978-2.08870.14381960.119615962X-RAY DIFFRACTION100
2.0887-2.39080.12231030.113616066X-RAY DIFFRACTION100
2.3908-3.01170.13721420.121616174X-RAY DIFFRACTION100
3.0117-29.81860.11511530.131516629X-RAY DIFFRACTION100

+
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