[English] 日本語
Yorodumi
- PDB-2lu1: pfsub2 solution NMR structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lu1
Titlepfsub2 solution NMR structure
ComponentsSubtilase
KeywordsHYDROLASE / Sub2 inhibitor prodomain
Function / homology
Function and homology information


microneme membrane / subtilisin / membrane protein ectodomain proteolysis / cytoplasmic vesicle / serine-type endopeptidase activity / plasma membrane
Similarity search - Function
Alpha-Beta Plaits - #2370 / Subtilisin-like protease 2, prodomain / Prodomain subtilisin 2 / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily ...Alpha-Beta Plaits - #2370 / Subtilisin-like protease 2, prodomain / Prodomain subtilisin 2 / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Subtilisin-like protease 2
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodSOLUTION NMR / simulated annealing
AuthorsHe, Y. / Chen, Y. / Ruan, B. / O'Brochta, D. / Bryan, P. / Orban, J.
CitationJournal: Proteins / Year: 2012
Title: Solution NMR structure of a sheddase inhibitor prodomain from the malarial parasite Plasmodium falciparum.
Authors: He, Y. / Chen, Y. / Oganesyan, N. / Ruan, B. / O'Brochta, D. / Bryan, P.N. / Orban, J.
History
DepositionJun 6, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Nov 14, 2012Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Subtilase


Theoretical massNumber of molelcules
Total (without water)17,7211
Polymers17,7211
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 acceptable covalent geometry
RepresentativeModel #1lowest energy

-
Components

#1: Protein Subtilase


Mass: 17721.326 Da / Num. of mol.: 1 / Fragment: sheddase inhibitor prodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: sub-2 / Plasmid: pPal7 / Production host: Escherichia coli (E. coli) / References: UniProt: O97364

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D C(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D 1H-15N NOESY
1813D 1H-13C NOESY aliphatic
1913D 1H-13C NOESY aromatic
11013D H(CCO)NH

-
Sample preparation

DetailsContents: 0.3 - 0.4 mM [U-13C; U-15N] pfsub2, 100 mM potassium phosphate, 10 mM sodium azide, 5 % D2O, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMpfsub2-1[U-13C; U-15N]0.3-0.41
100 mMpotassium phosphate-21
10 mMsodium azide-31
5 %D2O-41
Sample conditionsIonic strength: 0.1 / pH: 7 / Pressure: ambient / Temperature: 310 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR softwareName: CNS / Version: 1.21 / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 956 / NOE intraresidue total count: 601 / NOE long range total count: 88 / NOE medium range total count: 56 / NOE sequential total count: 211
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
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://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