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- PDB-6uf2: NMR structure of biofilm-related Se0862 from Synechococcus elongatus -

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Basic information

Entry
Database: PDB / ID: 6uf2
TitleNMR structure of biofilm-related Se0862 from Synechococcus elongatus
ComponentsBiofilm-related protein
KeywordsUNKNOWN FUNCTION / secretion / biofilm
Function / homologyTransposase
Function and homology information
Biological speciesSynechococcus elongatus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsZhang, N. / LiWang, A.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)FA9550-17-1-0447 United States
CitationJournal: Protein Sci. / Year: 2020
Title: Solution NMR structure of Se0862, a highly conserved cyanobacterial protein involved in biofilm formation.
Authors: Zhang, N. / Chang, Y.G. / Tseng, R. / Ovchinnikov, S. / Schwarz, R. / LiWang, A.
History
DepositionSep 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 18, 2021Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Biofilm-related protein


Theoretical massNumber of molelcules
Total (without water)14,4251
Polymers14,4251
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Biofilm-related protein


Mass: 14425.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942 / Gene: Synpcc7942_0862
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q31PX7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D HNCO
161isotropic13D HN(CA)CO
1171isotropic13D HBHA(CO)NH
1161isotropic13D (H)CCH(CO)NH
1151isotropic13D CC(CO)NH
1141isotropic12D (HB)CB(CDCG)HG
1131isotropic12D (HB)CB(CDCGCE)HE
1121isotropic13D IPAP-HNCO
1111isotropic13D 1H-15N NOESY
1101isotropic13D 1H-13C NOESY
191isotropic13D (H)CCH-COSY
181isotropic13D (H)CCH-COSY
171isotropic13D (H)CCH-TOCSY
1181isotropic14D 13C-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 0.6 mM [U-99% 13C; U-99% 15N] Se0862, 20 mM Tris, 100 mM NaCl, 5 mM TCEP, 95% H2O/5% D2O
Label: 15N_13C_Se0862 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMSe0862[U-99% 13C; U-99% 15N]1
20 mMTrisnatural abundance1
100 mMNaClnatural abundance1
5 mMTCEPnatural abundance1
Sample conditionsDetails: 20 mM Tris, 100 mM NaCl, 5 mM TCEP, / Ionic strength: 125 mM / Label: 15N_13C_Se0862 / pH: 7 / Pressure: 1013.25 mbar / Temperature: 295 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: TCI cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.51Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.51Schwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRFAM-SPARKY1.414Woonghee Lee, Marco Tonelli, and John L. Markleychemical shift assignment
NMRFAM-SPARKY1.414Woonghee Lee, Marco Tonelli, and John L. Markleypeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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