[English] 日本語
Yorodumi
- PDB-2kqa: The solution structure of the fungal elicitor Cerato-Platanin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kqa
TitleThe solution structure of the fungal elicitor Cerato-Platanin
ComponentsCerato-platanin
KeywordsTOXIN / elicitor / Secreted
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
Cerato-platanin / Cerato-platanin / RlpA-like domain / RlpA-like domain superfamily / Barwin-like endoglucanases / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesCeratocystis platani (fungus)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsOliveira, A.L. / Gallo, M. / Pazzagli, L. / Cappugi, G. / Scala, A. / Cicero, D.O. / Pantera, B. / Spisni, A. / Benedetti, C.E. / Pertinhez, T.A.
CitationJournal: To be Published
Title: The solution structure of the fungal elicitor Cerato-Platanin
Authors: Oliveira, A.L. / Gallo, M. / Pazzagli, L. / Cappugi, G. / Scala, A. / Cicero, D.O. / Pantera, B. / Spisni, A. / Benedetti, C.E. / Pertinhez, T.A.
History
DepositionNov 3, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cerato-platanin


Theoretical massNumber of molelcules
Total (without water)13,4361
Polymers13,4361
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 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Cerato-platanin


Mass: 13435.853 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ceratocystis platani (fungus) / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / References: UniProt: P81702

-
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 HNCA
1613D HN(CA)CB
1713D CBCA(CO)NH
1813D HN(CO)CA
1913D 1H-15N TOCSY
11013D 1H-13C NOESY
11113D 1H-15N NOESY
11212D 1H-15N HSQC
11313D HACACO

-
Sample preparation

DetailsContents: 0.7 mM [U-100% 13C; U-100% 15N] Cerato-Platanin, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
SampleConc.: 0.7 mM / Component: Cerato-Platanin-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 10 / pH: 5.8 / Pressure: ambient / Temperature: 293 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance7001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA5003

-
Processing

NMR software
NameDeveloperClassification
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMRViewJohnson, One Moon Scientificdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
AQUARullmann, Doreleijers and Kapteindata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
TALOSCornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Slightly modified to incorporate RDCs
NMR constraintsNOE constraints total: 3203 / NOE intraresidue total count: 1094 / NOE long range total count: 991 / NOE medium range total count: 406 / NOE sequential total count: 712
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / 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