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- PDB-2mog: Solution structure of the terminal Ig-like domain from Leptospira... -

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Basic information

Entry
Database: PDB / ID: 2mog
TitleSolution structure of the terminal Ig-like domain from Leptospira interrogans LigB
ComponentsBacterial Ig-like domain, group 2
KeywordsCELL ADHESION / Immunoglobulin-like fold / surface protein
Function / homologyImmunoglobulin-like - #1080 / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesLeptospira interrogans (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsPtak, C.P. / Hsieh, C. / Lin, Y. / Maltsev, A.S. / Raman, R. / Sharma, Y. / Oswald, R.E. / Chang, Y.
CitationJournal: Biochemistry / Year: 2014
Title: NMR Solution Structure of the Terminal Immunoglobulin-like Domain from the Leptospira Host-Interacting Outer Membrane Protein, LigB.
Authors: Ptak, C.P. / Hsieh, C.L. / Lin, Y.P. / Maltsev, A.S. / Raman, R. / Sharma, Y. / Oswald, R.E. / Chang, Y.F.
History
DepositionApr 25, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Jun 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
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: Bacterial Ig-like domain, group 2


Theoretical massNumber of molelcules
Total (without water)9,6411
Polymers9,6411
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Bacterial Ig-like domain, group 2 / LigB


Mass: 9641.489 Da / Num. of mol.: 1 / Fragment: Ig-like domain 12 (UNP residues 1029-1123)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans (bacteria) / Gene: LEP1GSC112_5106 / Plasmid: pET28-His-Sumo / Production host: Escherichia coli (E. coli) / References: UniProt: M6R7K6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1213D HN(CO)CA
1313D HN(CA)CO
1413D HNCA
1513D HNCO
1613D CBCANH
1713D HNCBCACO
1813D C(CO)NH
1913D H(CCO)NH
11023D 1H-15N TOCSY
11123D 1H-15N NOESY
11213D 1H-13C NOESY
11313D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-95% 13C; U-95% 15N] LigB, 137 mM sodium chloride, 10 mM sodium phosphate, 2.7 mM potassium chloride, 1.8 mM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-95% 15N] LigB, 137 mM sodium chloride, 10 mM sodium phosphate, 2.7 mM potassium chloride, 1.8 mM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMLigB-1[U-95% 13C; U-95% 15N]1
137 mMsodium chloride-21
10 mMsodium phosphate-31
2.7 mMpotassium chloride-41
1.8 mMpotassium phosphate-51
0.5 mMLigB-6[U-95% 15N]2
137 mMsodium chloride-72
10 mMsodium phosphate-82
2.7 mMpotassium chloride-92
1.8 mMpotassium phosphate-102
Sample conditionsIonic strength: 0.15 / pH: 7 / Pressure: ambient / Temperature: 286 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
VNMRVariancollection
XPLOR-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
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: 20

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