[English] 日本語
Yorodumi
- PDB-2jn4: Solution NMR Structure of Protein RP4601 from Rhodopseudomonas pa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jn4
TitleSolution NMR Structure of Protein RP4601 from Rhodopseudomonas palustris. Northeast Structural Genomics Consortium Target RpT2; Ontario Center for Structural Proteomics Target RP4601.
ComponentsHypothetical protein fixU, nifT
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / Rhodopseudomonas palustris / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyNifT/FixU-like / NifT/FixU / NifT/FixU barrel-like domain superfamily / NifT/FixU protein / nitrogen fixation / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodSOLUTION NMR / simulated annealing
AuthorsLemak, A. / Srisailam, S. / Yee, A. / Karra, M.D. / Lukin, J.A. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG)
Citation
Journal: To be Published
Title: Solution structure of a hypothetical protein RP4601 from Rhodopseudomonas palustris
Authors: Lemak, A. / Srisailam, S. / Yee, A. / Karra, M.D. / Lukin, J.A. / Arrowsmith, C.H.
#1: Journal: J.Biomol.Nmr / Year: 2011
Title: A novel strategy for NMR resonance assignment and protein structure determination.
Authors: Lemak, A. / Gutmanas, A. / Chitayat, S. / Karra, M. / Fares, C. / Sunnerhagen, M. / Arrowsmith, C.H.
History
DepositionDec 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 18, 2012Group: Database references
Revision 1.4Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.5Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.6Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.7May 8, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical protein fixU, nifT


Theoretical massNumber of molelcules
Total (without water)9,6881
Polymers9,6881
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 / 150structures with the lowest energy
RepresentativeModel #1all calculated structures submitted

-
Components

#1: Protein Hypothetical protein fixU, nifT


Mass: 9688.134 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: fixU/ nifT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Gold Magic / References: UniProt: Q6N0Y6

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D CBCA(CO)NH
1513D H(CCO)NH
161HBHACBCAcoNH 4D projection Reconstruction
171HCCCcoNH TOCSY 4D Projection Reconstruction
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11013D HN(COCA)CB
11123D (H)CCH-TOCSY (H-TOCSY)
1122(H)CCH-TOCSY (C-TOCSY)
11323D 1H-13C NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM [U-100% 13C, U-100% 15N] RP4601, 10MM NA ACETATE, 400MM NACL, 10MM ZNSO4, 10MM DTT, 0.01 NAN3, 1MM BENZAMIDINE, 90% H2O, 10% D2O90% H2O/10% D2O
20.7 mM [U-100% 13C, U-100% 15N] RP4601, 10MM NA ACETATE, 400MM NACL, 10MM ZNSO4, 10MM DTT, 0.01 NAN3, 1MM BENZAMIDINE, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMRP4601[U-100% 13C; U-100% 15N]1
0.6 mMRP4601[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 400mM NACL / pH: 5.0 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE8003

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Bruker Biospincollection
NMRPipe2.6Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.106Goddardpeak picking
Sparky3.106Goddarddata analysis
Sparky3.106Goddardchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: all calculated structures submitted
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / 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://pdbjlvh1.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