[English] 日本語
Yorodumi
- PDB-6szc: NMR structure of repeat domain 13 of the fibrillar adhesin CshA f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6szc
TitleNMR structure of repeat domain 13 of the fibrillar adhesin CshA from Streptococcus gordonii.
ComponentsSurface-associated protein CshA
KeywordsCELL ADHESION / Adhesin / Fibril / Novel / Repeat domain / Streptococcus
Function / homology
Function and homology information


GEVED domain / GEVED domain / CshA domain / Surface adhesin CshA, non-repetitive domain 2 / Surface adhesin CshA non-repetitive domain 2 / Surface adhesin CshA repetitive domain / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
Surface-associated protein CshA
Similarity search - Component
Biological speciesStreptococcus gordonii (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsHigman, V.A. / Back, C. / Crump, M.P. / Race, P.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE016690 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/L01386X/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M025624/1 United Kingdom
Royal SocietyUF080534 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The streptococcal multidomain fibrillar adhesin CshA has an elongated polymeric architecture.
Authors: Back, C.R. / Higman, V.A. / Le Vay, K. / Patel, V.V. / Parnell, A.E. / Frankel, D. / Jenkinson, H.F. / Burston, S.G. / Crump, M.P. / Nobbs, A.H. / Race, P.R.
History
DepositionOct 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.4Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Surface-associated protein CshA


Theoretical massNumber of molelcules
Total (without water)12,4811
Polymers12,4811
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4830 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Surface-associated protein CshA


Mass: 12480.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sample sequence includes N-terminal His-tag and disordered N-terminal of the polypeptide.
Source: (gene. exp.) Streptococcus gordonii (strain Challis / ATCC 35105 / BCRC 15272 / CH1 / DL1 / V288) (bacteria)
Strain: Challis / ATCC 35105 / BCRC 15272 / CH1 / DL1 / V288
Gene: cshA, SGO_0854 / Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A8AWJ3

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic13D HN(CA)CB
132isotropic13D CBCA(CO)NH
142isotropic13D HNCA
151isotropic13D HNHA
162isotropic13D HN(CO)CA
172isotropic13D HNCO
182isotropic1HN(CA)CO
192isotropic13D C(CO)NH
1102isotropic13D (H)CCH-TOCSY
1111isotropic115N TOCSY-HSQC
1131isotropic115N NOESY-HSQC
1142isotropic113C NOESY-HSQC
1152isotropic113C NOESY-HSQC aromatic
1162isotropic215N NOESY-HSQC
1172isotropic213C NOESY-HSQC
1183isotropic12D 1H-15N HSQC
1193isotropic12D 1H-1H TOCSY
1203isotropic12D 1H-1H NOESY

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution120 mg/mL [U-15N] CshA_RD13, 50 mM sodium chloride, 20 mM potassium phosphate, 90% H2O/10% D2O15N-CshA_RD1390% H2O/10% D2O
solution320 mg/mL [U-15N] CshA_RD13, 50 mM sodium chloride, 20 mM potassium phosphate, 100% D2O15N-CshA_RD13-D2O100% D2O
solution220 mg/mL [U-13C; U-15N] CshA_RD13, 50 mM sodium chloride, 20 mM potassium phosphate, 90% H2O/10% D2O15N13C-CshA_RD1390% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mg/mLCshA_RD13[U-15N]1
50 mMsodium chloridenatural abundance1
20 mMpotassium phosphatenatural abundance1
20 mg/mLCshA_RD13[U-15N]3
50 mMsodium chloridenatural abundance3
20 mMpotassium phosphatenatural abundance3
20 mg/mLCshA_RD13[U-13C; U-15N]2
50 mMsodium chloridenatural abundance2
20 mMpotassium phosphatenatural abundance2
Sample conditionsIonic strength: 70 mM / Label: Condition1 / pH: 7.5 / Pressure: 1 atm / Temperature: 293 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Varian VNMRSVarianVNMRS6001with cryogenic cold probe
Varian INOVAVarianINOVA9002with cryogenic cold probe

-
Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisCCPNchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure calculation
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
Details: standard ARIA calculation and water refinement protocol
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15

+
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://pdbjlvh1.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