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- PDB-2l1n: Solution NMR structure of the protein YP_399305.1 -

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Basic information

Entry
Database: PDB / ID: 2l1n
TitleSolution NMR structure of the protein YP_399305.1
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown function / DUF1823 / Hypothetical protein / Cyanobacteria / PSI-Biology / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG
Function / homologyProtein of unknown function DUF1823 / Protein of unknown function DUF1823 / Domain of unknown function (DUF1823) / Actin-binding Protein, T-fimbrin; domain 1 / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein
Function and homology information
Biological speciesSynechococcus elongatus (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 11
AuthorsMohanty, B. / Serrano, P. / Geralt, M. / Horst, R. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Solution NMR structure of the protein YP_399305.1
Authors: Mohanty, B. / Serrano, P. / Geralt, M. / Horst, R. / Wuthrich, K.
History
DepositionJul 30, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Structure summary
Revision 1.3Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)13,8571
Polymers13,8571
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 / 80target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Uncharacterized protein


Mass: 13856.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 7942 / Gene: Synpcc7942_0286 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q31RK1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N Resolved [1H,1H]-NOESY
12113Cali Resolved [1H,1H]-NOESY
13113Caro Resolved [1H,1H]-NOESY
1414D APSY-HACANH
1515D APSY-(HA)CA(CO)NH
1615D APSY-CBCA(CO)NH
1712D 1H-15N HSQC
1812D 1H-13C HSQC

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Sample preparation

DetailsContents: 1.1 mM [U-98% 13C; U-98% 15N] YP_399305.1, 95 % H2O, 5 % D2O, 50 mM sodium chloride, 20 mM sodium phosphate, 4.5 mM sodium azide, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMYP_399305.1-1[U-98% 13C; U-98% 15N]1
95 %H2O-21
5 %D2O-31
50 mMsodium chloride-41
20 mMsodium phosphate-51
4.5 mMsodium azide-61
Sample conditionsIonic strength: 0.113 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANACYANA3.0Guntert, Mumenthaler and Wuthrichstructure solution
MOLMOL2K.1Koradi, Billeter and Wuthrichanalysis and display of molecules
CARAKeller and Wuthrichchemical shift assignment
TopSpin1.3Bruker Biospincollection
TopSpin1.3Bruker Biospinprocessing
OPALLuginbuhl, Guntert, Billeter and Wuthrichrefinement
UNIO2.0.0(UNIO)-Torsten Herrmannpeak picking
UNIO2.0.0(UNIO)-Torsten Herrmannstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: CYANA3.0
NMR constraintsNOE constraints total: 2331 / NOE intraresidue total count: 604 / NOE long range total count: 476 / NOE medium range total count: 640 / NOE sequential total count: 611 / Protein phi angle constraints total count: 111 / Protein psi angle constraints total count: 119
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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