[English] 日本語
Yorodumi
- PDB-6msp: De novo Designed Protein Foldit3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6msp
TitleDe novo Designed Protein Foldit3
ComponentsDe novo Designed Protein Foldit3
KeywordsDE NOVO PROTEIN / de no designed foldit foldit3
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
AuthorsLiu, G. / Ishida, Y. / Swapna, G.V.T. / Kleinfelter, S. / Koepnick, B. / Baker, D. / Montelione, G.T.
CitationJournal: Nature / Year: 2019
Title: De novo protein design by citizen scientists.
Authors: Koepnick, B. / Flatten, J. / Husain, T. / Ford, A. / Silva, D.A. / Bick, M.J. / Bauer, A. / Liu, G. / Ishida, Y. / Boykov, A. / Estep, R.D. / Kleinfelter, S. / Norgard-Solano, T. / Wei, L. / ...Authors: Koepnick, B. / Flatten, J. / Husain, T. / Ford, A. / Silva, D.A. / Bick, M.J. / Bauer, A. / Liu, G. / Ishida, Y. / Boykov, A. / Estep, R.D. / Kleinfelter, S. / Norgard-Solano, T. / Wei, L. / Players, F. / Montelione, G.T. / DiMaio, F. / Popovic, Z. / Khatib, F. / Cooper, S. / Baker, D.
History
DepositionOct 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 3, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 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 1.4May 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: De novo Designed Protein Foldit3


Theoretical massNumber of molelcules
Total (without water)11,7251
Polymers11,7251
Non-polymers00
Water00
1


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

-
Components

#1: Protein De novo Designed Protein Foldit3


Mass: 11725.060 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-13C NOESY
121isotropic13D 1H-15N NOESY
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D HNCO
161isotropic13D (H)CCH-TOCSY
181isotropic12D 1H-15N HSQC
171isotropic12D 1H-13C HSQC

-
Sample preparation

DetailsType: solution / Contents: 0.3 mM [U-13C; U-15N] foldit3, 90% H2O/10% D2O
Details: The purified protein was dialyzed against 20 mM potassium phosphate (pH 6.5) and the protein concentration was adjusted to between 0.3-0.4 mM for NMR studies.
Label: 15N13C / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.3 mM / Component: foldit3 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 0.2 mM / Label: condition_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoStructureHuang, Tejero, Powers and Montelionerefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
SparkyGoddardpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: medoid
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