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- PDB-2jvu: Solution Structure of Dispersin from Enteroaggregative Escherichi... -

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Basic information

Entry
Database: PDB / ID: 2jvu
TitleSolution Structure of Dispersin from Enteroaggregative Escherichia coli
ComponentsDISPERSIN
KeywordsUNKNOWN FUNCTION / BETA SANDWICH
Function / homologyImmunoglobulin-like - #2290 / : / Immunoglobulin-like / Sandwich / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsVelarde, J.J. / Varney, K.M. / Farfan, K. / Dudley, D. / Inman, J.G. / Fletcher, J. / Weber, D.J. / Nataro, J.P.
CitationJournal: Mol.Microbiol. / Year: 2007
Title: Solution structure of the novel dispersin protein of enteroaggregative Escherichia coli.
Authors: Velarde, J.J. / Varney, K.M. / Inman, K.G. / Farfan, M. / Dudley, E. / Fletcher, J. / Weber, D.J. / Nataro, J.P.
History
DepositionSep 25, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Remark 999Sequence The sequence is not available in the UniProt database at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DISPERSIN


Theoretical massNumber of molelcules
Total (without water)11,3241
Polymers11,3241
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein DISPERSIN


Mass: 11324.377 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: EAEC 042 / Gene: AAP / Plasmid: PQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q08JB9
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1313D 13C- SEPARATED NOESY
1413D 15N- SEPARATED NOESY
1514D 13C- SEPARATED NOESY
1614D 13C/15N- SEPARATED NOESY
1713D 15N-EDITED HOHAHA-HSQC
1813D 15N
191EDITED HMQC-NOESY-HSQC
11013D 15N HNHA
11113D HNCO
11213D C(CO)NH
11313D CBCA(CO)NH
11413D HN(CA)CB
11513D HCA(CO)N
1161IPAP-HSQC
11713D HN(CO)CA
1181IPAP-HSQC
11913D HN(CO)CA

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Sample preparation

DetailsContents: 0.5-1.5 mM [U-100% 13C; U-100% 15N] DISPERSIN, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: DISPERSIN, AAP / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 45mM PHOS, 45mM NACL, 0.2mM EDTA / pH: 6.5 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: BRUKER DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XPLOR-NIH2.9.1SCHWIETERS, C.D. et al.refinement
NMRPipe1.8Delaglio, F. et al.processing
XwinNMR2.6Bruker Biospinprocessing
NMRDrawDelaglio, F. et al.peak picking
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: INITIAL NOE STRUCTURE REFINED WITH RESIDUAL DIPOLAR COUPLING DATA
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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