[English] 日本語
Yorodumi
- PDB-1ykg: Solution structure of the flavodoxin-like domain from the Escheri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ykg
TitleSolution structure of the flavodoxin-like domain from the Escherichia coli sulfite reductase
ComponentsSulfite reductase [NADPH] flavoprotein alpha-component
KeywordsELECTRON TRANSPORT / flavoprotein
Function / homology
Function and homology information


assimilatory sulfite reductase (NADPH) / sulfite reductase (NADPH) activity / sulfite reductase complex (NADPH) / riboflavin reductase (NADPH) activity / sulfate assimilation / hydrogen sulfide biosynthetic process / cysteine biosynthetic process / NADP+ binding / FMN binding / flavin adenine dinucleotide binding ...assimilatory sulfite reductase (NADPH) / sulfite reductase (NADPH) activity / sulfite reductase complex (NADPH) / riboflavin reductase (NADPH) activity / sulfate assimilation / hydrogen sulfide biosynthetic process / cysteine biosynthetic process / NADP+ binding / FMN binding / flavin adenine dinucleotide binding / oxidoreductase activity / cytosol
Similarity search - Function
Sulphite reductase [NADPH] flavoprotein, alpha chain / Sulphite reductase [NADPH] flavoprotein, alpha chain, Proteobacteria / Flavodoxin domain / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. ...Sulphite reductase [NADPH] flavoprotein, alpha chain / Sulphite reductase [NADPH] flavoprotein, alpha chain, Proteobacteria / Flavodoxin domain / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Sulfite reductase [NADPH] flavoprotein alpha-component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsSibille, N. / Blackledge, M. / Brutscher, B. / Coves, J. / Bersch, B.
Citation
Journal: Biochemistry / Year: 2005
Title: Solution Structure of the Sulfite Reductase Flavodoxin-like Domain from Escherichia coli
Authors: Sibille, N. / Blackledge, M. / Brutscher, B. / Coves, J. / Bersch, B.
#1: Journal: Biochemistry / Year: 2002
Title: Reactivity, secondary structure, and molecular topology of the Escherichia coli sulfite reductase flavodoxin-like domain
Authors: Champier, L. / Sibille, N. / Bersch, B. / Brutscher, B. / Blackledge, M. / Coves, J.
#2: Journal: J.BIOMOL.NMR / Year: 2001
Title: 1H, 13C, and 15N assignment of the flavodoxin-like domain of the Escherichia coli sulfite reductase
Authors: Sibille, N. / Coves, J. / Marion, D. / Brutscher, B. / Bersch, B.
History
DepositionJan 18, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sulfite reductase [NADPH] flavoprotein alpha-component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3482
Polymers17,8911
Non-polymers4561
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 15initial selection based on experimental energy target function
RepresentativeModel #2fewest violations

-
Components

#1: Protein Sulfite reductase [NADPH] flavoprotein alpha-component / SIR-FP


Mass: 17891.205 Da / Num. of mol.: 1 / Fragment: SiR-FP18, flavodoxin-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cysJ / Plasmid: pet30 / Production host: Escherichia coli (E. coli)
References: UniProt: P38038, assimilatory sulfite reductase (NADPH)
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
4113D 15N-separated NOESY
3213D 13C-separated NOESY
7312D NOESY
NMR detailsText: residual dipolar couplings and 3hJNC couplings for the detection of hydrogen-bonds have been measured using 3D-HNCO-type experiments.

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM U-15N, U-13C, 80%-2H SiR-FP18100mM phosphate buffer pH 7.0, H2O/D2O 90:10
21.5mM U-15N, U-13C, SiR-FP18100mM phosphate buffer pH 7.0, H2O/D2O 90:10
31.5mM U-15N, U-13C, SiR-FP18100mM phosphate buffer pH 7.0, D2O
41.5mM U-15N, SiR-FP18100mM phosphate buffer pH 7.0, H2O/D2O 90:10
51.5mM U-15N, U-13C, 80%-2H SiR-FP18100mM phosphate buffer pH 7.0, 2mM MgCl2, H2O/D2O 90:10, + 14mg/ml filamentous Pf1 phage
61.5mM U-15N, U-13C, 80%-2H SiR-FP18100mM phosphate buffer pH 7.0, H2O/D2O 90:10, +5% C12E5/hexanol with r=0.96
71.5mM U-15N, SiR-FP18100mM phosphate buffer pH 7.0, D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100mM phosphate buffer 7ambient 303 K
2100mM phosphate buffer, 2mM MgCl2 7ambient 303 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

-
Processing

NMR software
NameVersionDeveloperClassification
Discover2.98Accelrys Inc.structure solution
SCULPTOR1Hus, J.C., Blackledge, M.refinement
Felix2000Hare, F.processing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: residues 52-62 and 209-218 are disordered and are not included in the pdb file.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: initial selection based on experimental energy target function
Conformers calculated total number: 15 / Conformers submitted total number: 15

+
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