[English] 日本語
Yorodumi
- PDB-6llq: Solution NMR structure of de novo Rossmann2x2 fold with most of t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6llq
TitleSolution NMR structure of de novo Rossmann2x2 fold with most of the core mutated to valine, R2x2_VAL88
ComponentsVAL88
KeywordsDE NOVO PROTEIN / De Novo design
Biological speciesunidentified (others)
MethodSOLUTION NMR / simulated annealing
AuthorsKobayashi, N. / Sugiki, T. / Fujiwara, T. / Koga, R. / Yamamoto, M. / Kosugi, T. / Koga, N.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)15H05592 Japan
Japan Society for the Promotion of Science (JSPS)18H05420 Japan
Japan Science and TechnologyJPMJPR13AD Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101072 Japan
Japan Society for the Promotion of Science (JSPS)18K06152 Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Robust folding of a de novo designed ideal protein even with most of the core mutated to valine.
Authors: Koga, R. / Yamamoto, M. / Kosugi, T. / Kobayashi, N. / Sugiki, T. / Fujiwara, T. / Koga, N.
History
DepositionDec 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jun 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 1.3May 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: VAL88


Theoretical massNumber of molelcules
Total (without water)11,1061
Polymers11,1061
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7700 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

-
Components

#1: Protein VAL88


Mass: 11105.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HSQC aliphatic
131isotropic22D 1H-13C HSQC aromatic
141isotropic23D CBCA(CO)NH
151isotropic23D HN(CA)CB
161isotropic23D H(CCO)NH
171isotropic23D C(CO)NH
181isotropic23D 1H-15N NOESY
191isotropic23D 1H-13C NOESY aliphatic
1101isotropic13D 1H-13C NOESY aromatic
1131isotropic23D (H)CCH-TOCSY aliphatic
1112isotropic32D 1H-15N IPAP HSQC
1122anisotropic32D 1H-15N IPAP HSQC

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution1500 uM [U-99% 13C; U-99% 15N] VAL88, 7.4 mM potassium phosphate, 1.2 mM sodium phosphate, 100 mM sodium chloride, 95 % H2O, 5 % [U-99% 2H] D2O, 95% H2O/5% D2OVAL8895% H2O/5% D2O
solution2100 uM [U-99% 13C; U-99% 15N] VAL88, 7.4 mM potassium phosphate, 1.2 mM sodium phosphate, 100 mM sodium chloride, 10 mg/mL Pf1 phage, 95 % H2O, 5 % [U-99% 2H] D2O, 95% H2O/5% D2OVAL88-RDC95% H2O/5% D2OWeakly aligned
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMVAL88[U-99% 13C; U-99% 15N]1
7.4 mMpotassium phosphatenatural abundance1
1.2 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
95 %H2Onatural abundance1
5 %D2O[U-99% 2H]1
100 uMVAL88[U-99% 13C; U-99% 15N]2
7.4 mMpotassium phosphatenatural abundance2
1.2 mMsodium phosphatenatural abundance2
100 mMsodium chloridenatural abundance2
10 mg/mLPf1 phagenatural abundance2
95 %H2Onatural abundance2
5 %D2O[U-99% 2H]2
Sample conditionsIonic strength: 108.6 mM / Label: VAL88 / pH: 6 / Pressure: 1.0 atm / Temperature: 303 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002
Bruker AVANCE IIIBrukerAVANCE III9503

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView9Johnson, One Moon Scientificchemical shift assignment
MAGRO2.0.24Kobayashi, N.data analysis
CYANA3.98Guntert, Mumenthaler and Wuthrichchemical shift assignment
CYANA3.98Guntert, Mumenthaler and Wuthrichstructure calculation
TALOSTALOS+Yang, S. and Bax, Ad.data analysis
CYANA3.98Guntert, Mumenthaler and Wuthrichrefinement
MAGRO2.01.12Kobayashi, N. upgraded version of Kujira (Kobayshi, N. et al., 2007)data analysis
RefinementMethod: simulated annealing / Software ordinal: 8 / Details: refinment with RDC values as constrain
NMR representativeSelection criteria: target function
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