[English] 日本語
Yorodumi
- PDB-2jov: NMR Structure of Clostridium Perfringens Protein CPE0013. Northea... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jov
TitleNMR Structure of Clostridium Perfringens Protein CPE0013. Northeast Structural Genomics Target CpR31.
ComponentsHypothetical protein CPE0013Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha + beta sandwich / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyCPE0013-like fold / CPE0013-like / Protein of unknown function DUF1667 / CPE0013-like superfamily / Protein of unknown function (DUF1667) / Roll / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesClostridium perfringens (bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsDing, K. / Ramelot, T.A. / Anklin, C.G. / Wang, H. / Nwosu, C. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. ...Ding, K. / Ramelot, T.A. / Anklin, C.G. / Wang, H. / Nwosu, C. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR structure of Clostridium perfringens protein CPE0013.
Authors: Ding, K. / Ramelot, T.A. / Wang, H. / Nwosu, C. / Montelione, G.T. / Kennedy, M.A.
History
DepositionApr 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents ..._pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Jun 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 1.5Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.6May 8, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical protein CPE0013


Theoretical massNumber of molelcules
Total (without water)9,6791
Polymers9,6791
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 30structures with the lowest energy
RepresentativeModel #1lowest total energy

-
Components

#1: Protein Hypothetical protein CPE0013 / Hypothesis


Mass: 9679.284 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8XPF0

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HNCA
1413D HN(CO)CA
1513D CBCA(CO)NH
1613D HN(CA)CB
1722D 1H-13C HSQC
1832D 1H-13C HSQC
1913D HBHA(CO)NH
11023D (H)CCH-TOCSY
11113D 1H-15N NOESY
11213D 1H-13C NOESY
11323D 1H-13C NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM NaCl, 10 mM DTT, 5 mM CaCl2, 0.02 % NaN3, 5 % D2O, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM NaCl, 10 mM DTT, 5 mM CaCl2, 0.02 % NaN3, 100% D2O100% D2O
31 mM [U-5% 13C; U-100% 15N] protein, 20 mM MES, 100 mM NaCl, 10 mM DTT, 5 mM CaCl2, 0.02 % NaN3, 5 % D2O, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein[U-100% 13C; U-100% 15N]1
20 mMMES1
100 mMNaCl1
10 mMDTT1
5 mMCaCl21
0.02 %NaN31
5 %D2O1
1 mMprotein[U-100% 13C; U-100% 15N]2
20 mMMES2
100 mMNaCl2
10 mMDTT2
5 mMCaCl22
0.02 %NaN32
1 mMprotein[U-5% 13C; U-100% 15N]3
20 mMMES3
100 mMNaCl3
10 mMDTT3
5 mMCaCl23
0.02 %NaN33
5 %D2O3
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
X-PLOR NIH2.15.0Schwieters, Kuszewski, Tjandra and Clorestructure solution
AutoStructureHuang, Swapana, Rajan, Ke, Xia, Shukla, Inouye and Montelionedata analysis
SparkyGoddarddata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
Details: DGSA calculation using xplor NIH and then followed by CNS water refinement.
NMR representativeSelection criteria: lowest total energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / 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