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- PDB-7n82: NMR Solution structure of Se0862 -

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Basic information

Entry
Database: PDB / ID: 7n82
TitleNMR Solution structure of Se0862
ComponentsBiofilm-related protein
KeywordsUNKNOWN FUNCTION
Function / homology: / Uncharacterized protein
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: Proteins / Year: 2021
Title: Assessment of prediction methods for protein structures determined by NMR in CASP14: Impact of AlphaFold2.
Authors: Huang, Y.J. / Zhang, N. / Bersch, B. / Fidelis, K. / Inouye, M. / Ishida, Y. / Kryshtafovych, A. / Kobayashi, N. / Kuroda, Y. / Liu, G. / LiWang, A. / Swapna, G.V.T. / Wu, N. / Yamazaki, T. / Montelione, G.T.
History
DepositionJun 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 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: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 2000structures 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 (bacteria)
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
1151isotropic13D HN(CO)CA
1141isotropic13D HBHA(CO)NH
1131isotropic13D C(CO)NH
1121isotropic13D 1H-13C NOESY
1111isotropic13D 1H-15N NOESY
1101isotropic13D (H)CCH-COSY
1161isotropic13D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 0.6 mM [U-100% 13C; U-100% 15N] Se0862, 20 mM TRIS, 100 mM sodium chloride, 5 mM TCEP, 10 uM DSS, 0.02 % v/v sodium azide, 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-100% 13C; U-100% 15N]1
20 mMTRISnatural abundance1
100 mMsodium chloridenatural abundance1
5 mMTCEPnatural abundance1
10 uMDSSnatural abundance1
0.02 % v/vsodium azidenatural abundance1
Sample conditionsDetails: 20 mM tris 100mM 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 DMX / Manufacturer: Bruker / Model: AVANCE DMX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRFAM-SPARKYLee W, Tonelli M, Markley JLchemical shift assignment
NMRFAM-SPARKYLee W, Tonelli M, Markley JLpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 2000 / Conformers submitted total number: 20

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