[English] 日本語
Yorodumi
- PDB-2mr6: Solution NMR Structure of De novo designed protein, Northeast Str... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mr6
TitleSolution NMR Structure of De novo designed protein, Northeast Structural Genomics Consortium (NESG) Target OR462
ComponentsDe novo designed Protein OR462
KeywordsDE NOVO PROTEIN / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-Biology / Protein Structure Initiative
Function / homologyRossmann fold - #11230 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesartificial gene (others)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsXu, X. / Nivon, L. / Federizon, J.F. / Maglaqui, M. / Janjua, H. / Mao, L. / Xiao, R. / Kornhaber, G. / Baker, D. / Montelione, G.T. ...Xu, X. / Nivon, L. / Federizon, J.F. / Maglaqui, M. / Janjua, H. / Mao, L. / Xiao, R. / Kornhaber, G. / Baker, D. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of De novo designed protein, Northeast Structural Genomics Consortium (NESG) Target OR462
Authors: Xu, X. / Nivon, L. / Federizon, J.F. / Maglaqui, M. / Janjua, H. / Mao, L. / Xiao, R. / Kornhaber, G. / Baker, D. / Montelione, G.T. / Szyperski, T.
History
DepositionJul 1, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.2May 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 OR462


Theoretical massNumber of molelcules
Total (without water)15,7131
Polymers15,7131
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 De novo designed Protein OR462


Mass: 15712.907 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aromatic
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D simultaneous Cali,Caro, and N NOESY
181CCH-TOCSY
1913D HN(CA)CO
11012D 1H-13C HSQC aliphatic
11112D ct-1H-13C HSQC aliphatic
11212D ct-1H-13C HSQC aromatic
1131GFT(4,3d) HCCHCOSY ali
1141gft(4,3d) HCCHCOSY caro
11512D ct-1H-13C HSQC aliphatic 28ms
11612D ct-1H-13C HSQC aliphatic 28ms
11712D ct-1H-13C hscq aliphatic 42ms
11812D cr-1H-13C HSQC aliphatic 56ms

-
Sample preparation

DetailsContents: 1.2 mM OR462, 90% H2O/10% D2O,pH7.5 / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

-
Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis
AutoStructure2.1Huang, Tejero, Powers and Montelionerefinement
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
TopSpinBruker Biospincollection
VnmrJVariancollection
TALOSNShen, Cornilescu, Delaglio and Baxgeometry optimization
AS-DP1(AS-DP) Huang,Tejero,Powers, and Montelionedata analysis
AS-DP1(AS-DP) Huang,Tejero,Powers, and Montelionestructure solution
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichpeak picking
PSVSBhattacharya, Montelionestructure validation
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure determination was performed by running CYANA and ASDP in parallel using NOE-based constraints and PHI,PSI, and CHI1 dihedral angle constraints from TALOSN. Consensus peak ...Details: Structure determination was performed by running CYANA and ASDP in parallel using NOE-based constraints and PHI,PSI, and CHI1 dihedral angle constraints from TALOSN. Consensus peak assignments were selected and used in iterative refinement with CYANA. The 20 conformers out of 100 with the lowest target function were further refined by simulated annealing in explicit water bath using the program CNS with PARAM19 force field NMR Ensemble Information
NMR constraintsNOE constraints total: 2286 / NOE intraresidue total count: 538 / NOE long range total count: 783 / NOE medium range total count: 449 / NOE sequential total count: 516 / Protein chi angle constraints total count: 48 / Protein phi angle constraints total count: 100 / Protein psi angle constraints total count: 100
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://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