[English] 日本語
Yorodumi
- PDB-2n59: Solution Structure of R. palustris CsgH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2n59
TitleSolution Structure of R. palustris CsgH
ComponentsPutative uncharacterized protein CsgH
KeywordsUNKNOWN FUNCTION
Function / homologyImmunoglobulin-like - #2420 / Immunoglobulin-like / Sandwich / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesRhodopseudomonas palustris DX-1 (phototrophic)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model1
AuthorsHawthorne, W.J. / Taylor, J.D. / Escalera-Maurer, A. / Lambert, S. / Koch, M. / Scull, N. / Sefer, L. / Xu, Y. / Matthews, S.J.
CitationJournal: Sci Rep / Year: 2016
Title: Electrostatically-guided inhibition of Curli amyloid nucleation by the CsgC-like family of chaperones.
Authors: Taylor, J.D. / Hawthorne, W.J. / Lo, J. / Dear, A. / Jain, N. / Meisl, G. / Andreasen, M. / Fletcher, C. / Koch, M. / Darvill, N. / Scull, N. / Escalera-Maurer, A. / Sefer, L. / Wenman, R. / ...Authors: Taylor, J.D. / Hawthorne, W.J. / Lo, J. / Dear, A. / Jain, N. / Meisl, G. / Andreasen, M. / Fletcher, C. / Koch, M. / Darvill, N. / Scull, N. / Escalera-Maurer, A. / Sefer, L. / Wenman, R. / Lambert, S. / Jean, J. / Xu, Y. / Turner, B. / Kazarian, S.G. / Chapman, M.R. / Bubeck, D. / de Simone, A. / Knowles, T.P. / Matthews, S.J.
History
DepositionJul 13, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein CsgH


Theoretical massNumber of molelcules
Total (without water)11,1841
Polymers11,1841
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Putative uncharacterized protein CsgH


Mass: 11183.521 Da / Num. of mol.: 1 / Fragment: UNP residues 10-106
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris DX-1 (phototrophic)
Strain: DX-1 / Gene: csgH, Rpdx1_1250 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 Express / References: UniProt: E6VF87

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D HNCO
1513D HN(CA)CO
1613D HBHA(CO)NH
1713D CC(CO)NH
1813D (H)CCH-TOCSY
1922D 1H-13C HSQC aromatic
11022D 1H-1H NOESY
11123D 1H-13C NOESY
11213D 1H-15N NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
1400 uM [U-98% 13C; U-98% 15N] CsgH, 150 mM sodium chloride, 10 mM MES, 10 % [U-2H] D2O, 90% H2O/10% D2O90% H2O/10% D2O
2400 uM [U-98% 13C; U-98% 15N] CsgH, 150 mM sodium chloride, 10 mM MES, 100 % [U-2H] D2O, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMCsgH-1[U-98% 13C; U-98% 15N]1
150 mMsodium chloride-21
10 mMMES-31
10 %D2O-4[U-2H]1
400 uMCsgH-5[U-98% 13C; U-98% 15N]2
150 mMsodium chloride-62
10 mMMES-72
100 %D2O-8[U-2H]2
Sample conditionsIonic strength: 150 / pH: 6.5 / Pressure: ambient / Temperature: 292 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance6001
Bruker AvanceBrukerAvance8002
Bruker AvanceBrukerAvance9503

-
Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3Linge, O'Donoghue and Nilgesstructure solution
NMRView5.2.2Johnson, One Moon Scientificchemical shift assignment
CcpNmr2.4.0Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Ulrich EL, Markley JL, Ionides J, Laue ED.chemical shift assignment
CcpNmr2.4.0Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Ulrich EL, Markley JL, Ionides J, Laue ED.peak picking
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ARIArefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1721 / NOE intraresidue total count: 575 / NOE long range total count: 373 / NOE medium range total count: 54 / NOE sequential total count: 200 / Disulfide bond constraints total count: 1 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 85 / Protein psi angle constraints total count: 85
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 20 / Representative conformer: 1

+
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