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- PDB-2n7s: Solution Structure of Leptospiral LigA4 Big Domain -

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Basic information

Entry
Database: PDB / ID: 2n7s
TitleSolution Structure of Leptospiral LigA4 Big Domain
ComponentsIg-like repeat domain protein 1
KeywordsSTRUCTURAL PROTEIN / PDZ
Function / homology
Function and homology information


Immunoglobulin-like - #1080 / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig-like repeat domain protein 1 / Ig-like repeat domain protein 3
Similarity search - Component
Biological speciesLeptospira interrogans serovar Copenhageni str. Fiocruz L1-130 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsMei, S.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2015
Title: Solution structure of leptospiral LigA4 Big domain.
Authors: Mei, S. / Zhang, J. / Zhang, X. / Tu, X.
History
DepositionSep 17, 2015Deposition site: BMRB / Processing site: PDBJ
SupersessionOct 21, 2015ID: 2N2I
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
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: Ig-like repeat domain protein 1


Theoretical massNumber of molelcules
Total (without water)9,4811
Polymers9,4811
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 / 1799target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Ig-like repeat domain protein 1


Mass: 9481.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 (bacteria)
Strain: Fiocruz L1-130 / Gene: ligA, LIC_10465 / Production host: Escherichia coli (E. coli) / References: UniProt: G1UB65, UniProt: Q72V39*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-15N HSQC

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Sample preparation

DetailsContents: 100 mM sodium chloride-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 100 mM / Component: sodium chloride-1
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 20 K

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
PyMOLrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 1799 / Conformers submitted total number: 20 / Representative conformer: 1

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