[English] 日本語
Yorodumi
- PDB-8eo9: The solution structure of abxF, an enzyme catalyzing the formatio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8eo9
TitleThe solution structure of abxF, an enzyme catalyzing the formation of chiral spiroketal of an antibiotics, (-)-ABX
ComponentsGlyoxalaseGlyoxalase system
KeywordsBIOSYNTHETIC PROTEIN / CYANA 3.98.13 / enzyme / catalysis / chiral spiroketal
Function / homologyGlyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Glyoxalase
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsJia, X. / Yan, X. / Mobli, M. / Qu, X.
Funding support Australia, China, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP220103028 Australia
National Science Foundation (NSF, China)1800048 China
CitationJournal: To Be Published
Title: The solution structure of abxF, an enzyme catalyzing the formation of chiral spiroketal of an antibiotics, (-)-ABX.
Authors: Jia, X. / Yan, X. / Mobli, M. / Qu, X.
History
DepositionOct 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glyoxalase


Theoretical massNumber of molelcules
Total (without water)25,1921
Polymers25,1921
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

-
Components

#1: Protein Glyoxalase / Glyoxalase system


Mass: 25191.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Gene: abxF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2I6B3F9

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-13C HSQC aliphatic
121isotropic12D 1H-13C HSQC aromatic
131isotropic22D 1H-15N HSQC
141isotropic12D 1H-15N HSQC
152isotropic12D 1H-1H NOESY
1132isotropic12D 1H-15N HSQC
161isotropic13D 1H-13C NOESY aliphatic
171isotropic13D 1H-13C NOESY aromatic
181isotropic13D 1H-15N NOESY
191isotropic13D HNCO
1101isotropic13D HNCA
1111isotropic13D HN(CA)CB
1121isotropic13D HBHA(CO)NH
1141isotropic13D CBCA(CO)NH
1151isotropic13D HN(CO)CA
1161isotropic13D HN(CA)CO
1171isotropic13D (H)CCH-TOCSY
1181isotropic13D (H)CCH-TOCSY
1191isotropic12D hbcbcgcdcehegp
1201isotropic12D hbcbcgcdhdgp
1211anisotropic12d hbcbcgcchargp

-
Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11.25 mM [U-13C; U-15N] abxF, 5 % v/v [U-100% 2H] D2O, 95 % v/v H2O, 50 mM sodium chloride, 20 mM sodium phosphate, 3 mM sodium azide, 5 mM DTT, 95% H2O/5% D2O1.25 mM abxF in 20 mM sodium phosphate, 50 mM NaCl, 5 mM DTT, 3 mM NaN3, pH 6.6.13C,15N_abxF95% H2O/5% D2O
solution21.71 mM [U-100% 15N] abxF, 5 % v/v [U-100% 2H] D2O, 95 % v/v H2O, 50 mM sodium chloride, 20 mM sodium phosphate, 3 mM sodium azide, 5 mM DTT, 95% H2O/5% D2O1.71 mM abxF in 20 mM sodium phosphate, 50 mM NaCl, 5 mM DTT, 3 mM NaN3, pH 6.6.15N_abxF95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.25 mMabxF[U-13C; U-15N]1
5 % v/vD2O[U-100% 2H]1
95 % v/vH2Onatural abundance1
50 mMsodium chloridenatural abundance1
20 mMsodium phosphatenatural abundance1
3 mMsodium azidenatural abundance1
5 mMDTTnatural abundance1
1.71 mMabxF[U-100% 15N]2
5 % v/vD2O[U-100% 2H]2
95 % v/vH2Onatural abundance2
50 mMsodium chloridenatural abundance2
20 mMsodium phosphatenatural abundance2
3 mMsodium azidenatural abundance2
5 mMDTTnatural abundance2
Sample conditionsDetails: 20 mM sodium phosphate, 50 mM NaCl, 5 mM DTT, 3 mM NaN3, pH 6.6
Ionic strength: 20 mM sodium phosphate, 50 mM NaCl mM / Label: conditon_1 / pH: 6.6 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker AVANCEBrukerAVANCE7002

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.13Guntert, Mumenthaler and Wuthrichrefinement
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr AnalysisVersion 2.4.2CCPNchemical shift assignment
CcpNmr AnalysisVersion 2.4.2CCPNpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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