[English] 日本語
Yorodumi
- PDB-2jnv: Solution structure of C-terminal domain of NifU-like protein from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jnv
TitleSolution structure of C-terminal domain of NifU-like protein from Oryza sativa
ComponentsNifU-like protein 1, chloroplast
KeywordsMETAL TRANSPORT / iron-sulfur cluster binding / program for rice genome reserch / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


protein maturation by [4Fe-4S] cluster transfer / iron-sulfur cluster assembly / chloroplast stroma / 4 iron, 4 sulfur cluster binding / iron ion binding / mitochondrion
Similarity search - Function
NIF system FeS cluster assembly, NifU, C-terminal / NifU-like domain / Fe-S cluster assembly (FSCA) / Fe-S cluster assembly domain superfamily / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NifU-like protein 1, chloroplastic
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, torsion angle dynamics
AuthorsSaio, T. / Ogura, K. / Kumeta, H. / Yokochi, M. / Katoh, S. / Katoh, E. / Inagaki, F. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biochem.(Tokyo) / Year: 2007
Title: The cooperative role of OsCnfU-1A domain I and domain II in the iron sulphur cluster transfer process as revealed by NMR
Authors: Saio, T. / Kumeta, H. / Ogura, K. / Yokochi, M. / Asayama, M. / Katoh, S. / Katoh, E. / Teshima, K. / Inagaki, F.
History
DepositionFeb 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NifU-like protein 1, chloroplast


Theoretical massNumber of molelcules
Total (without water)9,8231
Polymers9,8231
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein NifU-like protein 1, chloroplast / OsNifu1


Mass: 9823.238 Da / Num. of mol.: 1 / Fragment: residues 73-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: NIFU1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q84LK7

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2112D 1H-15N HSQC
2212D 1H-13C HSQC
2313D HNCO
2413D HNCA
2513D HN(CO)CA
2613D HN(CA)CB
2713D CBCA(CO)NH
2813D HN(CA)HA
2913D HBHA(CO)NH
21013D CCH-TOCSY
21113D (H)CCH-TOCSY
21212D (HB)CB(CGCD)HD
21312D (HB)CB(CGCDCE)HE
11412D 1H-15N HSQC
11512D 1H-13C HSQC
11613D 1H-15N NOESY
11713D 1H-13C NOESY

-
Sample preparation

DetailsContents: 20 mM sodium phosphate, 150 mM sodium chloride, 0.02 w/v DSS, 10 % D2O, 10 mM DTT, 0.6 mM [U-98% 13C; U-98% 15N] OsNifU1A domain I (73-153), 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphate1
150 mMsodium chloride1
0.02 w/vDSS1
10 %D2O1
10 mMDTT1
0.6 mMOsNifU1A domain I (73-153)[U-98% 13C; U-98% 15N]1
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11507ambient 298 K
21507.5ambient 298 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Olivia1.13.1Yokochi, Sekiguchi and Inagakidata analysis
Olivia1.13.1Yokochi, Sekiguchi and Inagakichemical shift assignment
Olivia1.13.1Yokochi, Sekiguchi and Inagakipeak picking
VNMR6.1cVariancollection
NMRPipe23Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: DGSA-distance geometry simulated annealing, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
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://pdbjlc1.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