[English] 日本語
Yorodumi
- PDB-7tz8: Solution NMR structure of the PBS linker polypeptide domain (frag... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7tz8
TitleSolution NMR structure of the PBS linker polypeptide domain (fragment 254-400) of phycobilisome linker protein ApcE from Synechocystis sp. PCC 6803 refined with NH RDCs. Northeast Structural Genomics Consortium Target SgR209C
ComponentsPhycobiliprotein ApcE
KeywordsLYASE / slr0335 / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Lyases / phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis / lyase activity
Similarity search - Function
Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
Phycobiliprotein ApcE
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsRamelot, T.A. / Tejero, R. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: Front Mol Biosci / Year: 2022
Title: AlphaFold Models of Small Proteins Rival the Accuracy of Solution NMR Structures.
Authors: Tejero, R. / Huang, Y.J. / Ramelot, T.A. / Montelione, G.T.
History
DepositionFeb 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phycobiliprotein ApcE


Theoretical massNumber of molelcules
Total (without water)17,8681
Polymers17,8681
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1medoid

-
Components

#1: Protein Phycobiliprotein ApcE / Phycobilisome LCM core-membrane linker polypeptide / Phycobilisome core-membrane linker phycobiliprotein ApcE


Mass: 17868.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: apcE, slr0335 / Plasmid: pET21-23C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pMGK / References: UniProt: Q55544

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: isotropic / Type: 1D 1H

-
Sample preparation

DetailsType: solution
Contents: 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 100 mM DTT, 0.02 % sodium azide, 1.4 mM [U-100% 13C; U-100% 15N] protein, 95% H2O/5% D2O
Label: NC sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMMESnatural abundance2
100 mMsodium chloridenatural abundance2
5 mMcalcium chloridenatural abundance2
100 mMDTTnatural abundance2
0.02 %sodium azidenatural abundance2
1.4 mMprotein[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 200 mM / Label: 1 / pH: 6.5 / Pressure: 1 atm / Temperature: 293 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA3.98.14Guntert, Mumenthaler and Wuthrichstructure calculation
NMRFAM-SPARKY1.37Lee, Westler, Bahrami, Eghbalnia, Markleychemical shift assignment
PdbStat5.21.6Tejero, Snyder, Mao, Aramini, Montelionedata analysis
NMRFAM-SPARKY1.37Lee, Westler, Bahrami, Eghbalnia, Markleypeak picking
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: CNS water refinement
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
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