[English] 日本語
Yorodumi
- PDB-2n69: NMR structure of non-sweet mutant (ins18RI19) of sweet protein Br... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2n69
TitleNMR structure of non-sweet mutant (ins18RI19) of sweet protein Brazzein
ComponentsDefensin-like protein
KeywordsPLANT PROTEIN / Brazzein / Sweet protein
Function / homology
Function and homology information


defense response to fungus / killing of cells of another organism / defense response to bacterium / extracellular region
Similarity search - Function
Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Defensin-like protein
Similarity search - Component
Biological speciesPentadiplandra brazzeana (plant)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model1
AuthorsSingarapu, K.K. / Tonelli, M. / Markley, J.L. / Assadi-Porter, F.
CitationJournal: To be Published
Title: NMR Structure of sweeter mutant of sweet protein Brazzein
Authors: Singarapu, K.K. / Tonelli, M. / Markley, J.L. / Assadi-Porter, F.
History
DepositionAug 14, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Derived calculations / Category: struct_conf / struct_conf_type
Revision 1.2Dec 11, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: pdbx_nmr_software / pdbx_validate_close_contact ...pdbx_nmr_software / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif
Item: _pdbx_nmr_software.name / _struct_ref_seq_dif.details
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Defensin-like protein


Theoretical massNumber of molelcules
Total (without water)6,7791
Polymers6,7791
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 Defensin-like protein / Brazzein


Mass: 6778.710 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pentadiplandra brazzeana (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: P56552

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D (H)CCH-TOCSY
1713D H(CCO)NH
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11013D 1H-13C NOESY aromatic

-
Sample preparation

DetailsContents: 1.5 mM [U-100% 13C; U-100% 15N] Brz_RI-1, 1.5 mM [U-100% 13C; U-100% 15N] Brz_RI-2, 1.5 mM [U-100% 13C; U-100% 15N] Brz_RI-3, 1.5 mM [U-100% 13C; U-100% 15N] Brz_RI-4, 1.5 mM [U-100% 13C; U- ...Contents: 1.5 mM [U-100% 13C; U-100% 15N] Brz_RI-1, 1.5 mM [U-100% 13C; U-100% 15N] Brz_RI-2, 1.5 mM [U-100% 13C; U-100% 15N] Brz_RI-3, 1.5 mM [U-100% 13C; U-100% 15N] Brz_RI-4, 1.5 mM [U-100% 13C; U-100% 15N] Brz_RI-5, 1.5 mM [U-100% 13C; U-100% 15N] Brz_RI-6, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMBrz_RI-1[U-100% 13C; U-100% 15N]1
1.5 mMBrz_RI-2[U-100% 13C; U-100% 15N]1
1.5 mMBrz_RI-3[U-100% 13C; U-100% 15N]1
1.5 mMBrz_RI-4[U-100% 13C; U-100% 15N]1
1.5 mMBrz_RI-5[U-100% 13C; U-100% 15N]1
1.5 mMBrz_RI-6[U-100% 13C; U-100% 15N]1
Sample conditionsIonic strength: 0 / pH: 5.2 / Pressure: ambient / Temperature: 310 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
MOLMOLKoradi, Billeter and Wuthrichdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
PSVSBhattacharya and Montelionedata analysis
SparkyGoddarddata analysis
TALOSCornilescu, Delaglio and Baxstructure solution
XEASYBartels et al.data analysis
CYANArefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

+
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