[English] 日本語
Yorodumi
- PDB-2lt5: Zymogen-FLG of the onconase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lt5
TitleZymogen-FLG of the onconase
ComponentsProtein P-30
KeywordsHYDROLASE / ribonuclease
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA nuclease activity / endonuclease activity / nucleic acid binding / defense response to Gram-positive bacterium
Similarity search - Function
Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease
Similarity search - Domain/homology
Biological speciesRana pipiens (northern leopard frog)
MethodSOLUTION NMR / energy minimization
Model detailslowest energy, model 1
AuthorsVilanova, M. / Callis, M. / Laurents, D.V. / Ribo, M. / Bruix, M. / Serrano, S.
History
DepositionMay 14, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Feb 20, 2013Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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 / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein P-30


Theoretical massNumber of molelcules
Total (without water)13,2431
Polymers13,2431
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Protein P-30 / Onconase


Mass: 13243.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rana pipiens (northern leopard frog) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P22069, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D CBCANH
1413D HNCA
1513D HN(CO)CA
1613D HN(CA)CO
1713D 1H-13C NOESY
1813D 1H-15N NOESY
1913D HNCO
11012D 1H-13C HSQC
21122D 1H-13C HSQC
11212D 1H-1H NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
125 uL buffer 10x, 200 uL H2O MQ, 2 uL DSS, 2 uL NaN3, 2.8 mM [U-100% 15N, 13C] ONC_FLG, 90% H2O/10% D2O90% H2O/10% D2O
225 uL buffer 10x, 200 uL [U-100% 2H] D2O, 2 uL DSS, 2 uL NaN3, 1.8 mM [U-100% 15N] ONC_FLG, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 %buffer 10x-11
200 %H2O MQ-21
2 %DSS-31
2 %NaN3-41
2.8 mMONC_FLG-5[U-100% 15N, 13C]1
25 %buffer 10x-62
200 %D2O-7[U-100% 2H]2
2 %DSS-82
2 %NaN3-92
1.8 mMONC_FLG-10[U-100% 15N]2
Sample conditions
Conditions-IDPressure (kPa)Temperature (K)
1ambient 308 K
2ambient 303 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Bruker Biospinprocessing
TopSpin1.3Bruker Biospinacquisition
Sparky3.113Goddardchemical shift assignment
Sparky3.113Goddardpeak picking
TALOSTALOS +Cornilescu, Delaglio and Baxangular constraints
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
RefinementMethod: energy minimization / Software ordinal: 1 / Details: Gibbs Boltzmann minimization
NMR constraintsNOE constraints total: 2025 / NOE long range total count: 678 / NOE medium range total count: 288
NMR representativeSelection criteria: lowest energy
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