[English] 日本語
Yorodumi
- PDB-2kdn: Solution structure of PFE0790c, a putative bolA-like protein from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kdn
TitleSolution structure of PFE0790c, a putative bolA-like protein from the protozoan parasite Plasmodium falciparum.
ComponentsPutative uncharacterized protein PFE0790c
KeywordsUNKNOWN FUNCTION / NMR solution structure / SSGCID / Seattle Structural Genomics Center for Infectious Disease / structural genomics / malaria
Function / homology
Function and homology information


protein maturation by iron-sulfur cluster transfer / iron-sulfur cluster binding / 2 iron, 2 sulfur cluster binding / intracellular iron ion homeostasis / nucleus / cytosol
Similarity search - Function
BolA-like protein 2 / BolA-like / BolA protein / BolA-like superfamily / BolA-like protein / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BolA-like protein, putative
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
AuthorsBuchko, G.W. / Yee, A. / Semesi, A. / Hui, R. / Arrowsmith, C.H. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Solution-state NMR structure of the putative morphogene protein BolA (PFE0790c) from Plasmodium falciparum.
Authors: Buchko, G.W. / Yee, A. / Semesi, A. / Myler, P.J. / Arrowsmith, C.H. / Hui, R.
History
DepositionJan 12, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 6, 2015Group: Database references
Revision 1.3May 13, 2015Group: Database references
Revision 1.4May 20, 2015Group: Database references
Revision 1.5May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / 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_software.name / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein PFE0790c


Theoretical massNumber of molelcules
Total (without water)12,3281
Polymers12,3281
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 #1closest to the average

-
Components

#1: Protein Putative uncharacterized protein PFE0790c


Mass: 12328.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PFE0790c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8I3V0

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D HNCA
1513D 1H-15N NOESY
1613D HBHA(CO)NH
1713D 1H-13C NOESY
1813D C(CO)NH
1913D H(CCO)NH
11012D 1H-15N HSQC
11122D 1H-13C HSQC
11213D (H)CCH-TOCSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM [U-99% 13C; U-99% 15N] protein, 10 mM sodium phosphate, 200 mM sodium chloride, 10 mM DTT, 0.01 % sodium azide, 1 mM benzamidine, 93% H2O/7% D2O93% H2O/7% D2O
21.5 mM [U-7% 13C; U-99% 15N] protein, 10 mM sodium phosphate, 200 mM sodium chloride, 10 mM DTT, 0.01 % sodium azide, 1 mM benzamidine, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMprotein[U-99% 13C; U-99% 15N]1
10 mMsodium phosphate1
200 mMsodium chloride1
10 mMDTT1
0.01 %sodium azide1
1 mMbenzamidine1
1.5 mMprotein[U-7% 13C; U-99% 15N]2
10 mMsodium phosphate2
200 mMsodium chloride2
10 mMDTT2
0.01 %sodium azide2
1 mMbenzamidine2
Sample conditionsIonic strength: 200 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA8003

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, P. et al.structure solution
Sparky3.11Goddard, T. et al.data analysis
Sparky3.11Goddard, T. et al.peak picking
Felix2007Accelrys Software Inc.processing
CNS1.1Brunger, A. et al.refinement
CNS1.1Brunger, A. et al.structure solution
PSVS1.3Bhattacharya, A. et al.data analysis
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
Details: Structure determination was performed iteratively using CYANA (Automated NOESY Assignments). A total of 20 structures out of 100 with lowest target function from the final CYANA calculation ...Details: Structure determination was performed iteratively using CYANA (Automated NOESY Assignments). A total of 20 structures out of 100 with lowest target function from the final CYANA calculation were taken and refined by restrained molecular dynamics/energy minimization in explicit water (CNS) after adding 15% to the upper boundary limit. The final set of structures contained no dihedral violations greater than 1 degree and only 4 distance violations total that were greater than 0.05 Angstrom.
NMR constraintsNOE constraints total: 1619 / NOE intraresidue total count: 425 / NOE long range total count: 319 / NOE medium range total count: 399 / NOE sequential total count: 476 / Hydrogen bond constraints total count: 60 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 63 / Protein psi angle constraints total count: 63
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / 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