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- PDB-5jtk: NMR structure of Uncharacterized protein from Pseudomonas aerugin... -

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Basic information

Entry
Database: PDB / ID: 5jtk
TitleNMR structure of Uncharacterized protein from Pseudomonas aeruginosa PAO1
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homologyTsi6 / Tsi6 / protein secretion by the type VI secretion system / toxin sequestering activity / Immune protein Tsi6
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBarnwal, R.P. / Varani, G. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: NMR structure of Uncharacterized protein from Pseudomonas aeruginosa PAO1
Authors: Barnwal, R.P. / Varani, G.
History
DepositionMay 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_nmr_refine / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_prerelease_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_nmr_refine.method / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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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)10,6931
Polymers10,6931
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein Uncharacterized protein


Mass: 10693.325 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA0092 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I740

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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 HNCO
141isotropic13D HN(CA)CB
151isotropic13D CBCA(CO)NH
1141isotropic13D HBHA(CO)NH
1131isotropic23D 1H-15N NOESY
1121isotropic23D 1H-13C NOESY
1111isotropic13D (H)CCH-TOCSY
1101isotropic13D H(CCO)NH
1151isotropic22D 1H-1H NOESY

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Sample preparation

DetailsType: solution
Contents: 1.1 mM [U-98% 13C; U-98% 15N] Uncharacterized protein, 95% H2O/5% D2O
Label: 13C, 15N / Solvent system: 95% H2O/5% D2O
SampleConc.: 1.1 mM / Component: Uncharacterized protein / Isotopic labeling: [U-98% 13C; U-98% 15N]
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 6.0 / Pressure: AMBIENT Pa / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.97GUNTERT, MUMENTHALER AND WUTHRICHrefinement
CYANA3.97GUNTERT, MUMENTHALER AND WUTHRICHstructure calculation
CcpNMRCCPNchemical shift assignment
TopSpinBruker Biospincollection
CcpNMRCCPNpeak picking
TopSpinBruker Biospinprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10

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