[English] 日本語
Yorodumi
- PDB-2apn: hi1723 solution structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2apn
Titlehi1723 solution structure
ComponentsProtein HI1723
KeywordsStructural Genomics / UNKNOWN FUNCTION / hi1723 solution structure / Structure 2 Function Project / S2F
Function / homology
Function and homology information


: / iron-sulfur cluster assembly / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / iron ion binding / cytosol
Similarity search - Function
FeS cluster insertion protein ErpA / FeS cluster insertion, C-terminal, conserved site / Hypothetical hesB/yadR/yfhF family signature. / FeS cluster insertion protein / Hypothetical Protein Aq_1857; Chain: A; / HesB-like domain / FeS cluster biogenesis / HesB-like domain superfamily / Iron-sulphur cluster biosynthesis / Sandwich / Mainly Beta
Similarity search - Domain/homology
Iron-sulfur cluster insertion protein ErpA
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodSOLUTION NMR / CNS 1.1
AuthorsHe, Y. / Yeh, D.C. / Orban, J. / Structure 2 Function Project (S2F)
CitationJournal: To be Published
Title: Solution NMR Structure of HI1723 From Haemophilus Influenzae
Authors: He, Y. / Yeh, D.C. / Orban, J.
History
DepositionAug 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein HI1723


Theoretical massNumber of molelcules
Total (without water)12,2011
Polymers12,2011
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 least restraint violations
RepresentativeModel #1lowest energy

-
Components

#1: Protein Protein HI1723


Mass: 12200.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P45344

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
2223D 15N-separated NOESY
3333D HN(CA)CB, 3DHNCO, 3DCBCACONH, 3DHBHA(CBCACO)NH, 3D(H)C(CO)NH-TOCSY, H(CCO)NH-TOCSY, 2DTOCSY, 2D-CBHD, 2DCBHE, 2DTOCSY

-
Sample preparation

DetailsContents: 50 mM potassium phosphate, 100 mM sodium chloride, 4 mM DTT, pH7, 90% H2O with 10% D2O
Solvent system: 90% H2O with 10% D2O
Sample conditionsIonic strength: 50 ~ 100 mM / pH: 7 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX5002

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5Brukercollection
NMRPipeFrank Delaglio Stephan Grzeiek, Guang Zhu, Geerten W. Vuister, John Pfeifer, and Ad Baxprocessing
Sparky3T. D. Goddard and D. G. Kneller, SPARKY 3, University of California, San Franciscoprocessing
CNS1.1A. T. Brunger, P. D. Adams, G. M. Clore, W. L. Delano, P. Gros, R. W. Grosse-Kunsteve, J. S. Jiang, J. Kuszewski, M. Nilges, N. S. Pannu, R. J.Read, L. M. Rice, T. Simonson, G. L. Warrenstructure solution
CNS1.1A. T. Brunger, P. D. Adams, G. M. Clore, W. L. Delano, P. Gros, R. W. Grosse-Kunsteve, J. S. Jiang, J. Kuszewski, M. Nilges, N. S. Pannu, R. J.Read, L. M. Rice, T. Simonson, G. L. Warrenrefinement
RefinementMethod: CNS 1.1 / Software ordinal: 1 / Details: simulated annealing
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
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