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- PDB-2mpw: Solution structure of the LysM region of the E. coli Intimin peri... -

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Basic information

Entry
Database: PDB / ID: 2mpw
TitleSolution structure of the LysM region of the E. coli Intimin periplasmic domain
ComponentsIntimin
KeywordsPEPTIDOGLYCAN BINDING PROTEIN
Function / homology
Function and homology information


cell outer membrane / cell adhesion
Similarity search - Function
Intimin, C-terminal / Intimin C-type lectin domain / Intimin/invasin bacterial adhesion mediator protein / Inverse autotransporter, beta-domain / Inverse autotransporter, beta-domain superfamily / Bacterial Ig-like domain (group 1) / Inverse autotransporter, beta-domain / Bacterial Ig-like domain (group 1) / Big-1 (bacterial Ig-like domain 1) domain / Big-1 (bacterial Ig-like domain 1) domain profile. ...Intimin, C-terminal / Intimin C-type lectin domain / Intimin/invasin bacterial adhesion mediator protein / Inverse autotransporter, beta-domain / Inverse autotransporter, beta-domain superfamily / Bacterial Ig-like domain (group 1) / Inverse autotransporter, beta-domain / Bacterial Ig-like domain (group 1) / Big-1 (bacterial Ig-like domain 1) domain / Big-1 (bacterial Ig-like domain 1) domain profile. / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Lysin motif / LysM domain / LysM domain profile. / LysM domain / C-type lectin-like/link domain superfamily / C-type lectin fold / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing, NOESY back-calculation
Model detailsminimized average structure, model1
Model type detailsminimized average
AuthorsColes, M. / Chaubey, M. / Leo, J.C. / Linke, D. / Schuetz, M.C. / Goetz, F. / Autenrieth, I.B.
CitationJournal: Mol.Microbiol. / Year: 2015
Title: The Intimin periplasmic domain mediates dimerisation and binding to peptidoglycan.
Authors: Leo, J.C. / Oberhettinger, P. / Chaubey, M. / Schutz, M. / Kuhner, D. / Bertsche, U. / Schwarz, H. / Gotz, F. / Autenrieth, I.B. / Coles, M. / Linke, D.
History
DepositionJun 5, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: 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 / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Intimin


Theoretical massNumber of molelcules
Total (without water)12,5681
Polymers12,5681
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)23 / 95structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Intimin / / Attaching and effacing protein / Eae protein


Mass: 12568.167 Da / Num. of mol.: 1 / Fragment: LysM region (UNP residues 39-143) / Mutation: A39M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: eae, eaeA, E2348C_3939 / Plasmid: pASK-IBA / Production host: Escherichia coli (E. coli) / References: UniProt: P19809

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D HNCO
1223D HNCA
1323D C(CO)NH
1423D HNCANNH
1523D (H)CCH-TOCSY
1623D H(CCO)NH
1713D 1H-15N NOESY
1823D 1H-13C NOESY
1923D CNH-NOESY
11013D NNH-NOESY
11123D CCH-NOESY
11212D 12C-filtered 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 15N] LysM, 20 mM sodium phosphate, 150 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C; U-100% 15N] LysM, 20 mM sodium phosphate, 150 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMLysM-1[U-100% 15N]1
20 mMsodium phosphate-21
150 mMsodium chloride-31
0.5 mMLysM-4[U-100% 13C; U-100% 15N]2
20 mMsodium phosphate-52
150 mMsodium chloride-62
Sample conditionsIonic strength: 250 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMR-SPIRIT1.1In-houserefinement
RefinementMethod: simulated annealing, NOESY back-calculation / Software ordinal: 1
NMR constraintsProtein chi angle constraints total count: 47 / Protein other angle constraints total count: 168 / Protein phi angle constraints total count: 88 / Protein psi angle constraints total count: 49
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 95 / Conformers submitted total number: 23 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 0.4 ° / Maximum upper distance constraint violation: 0.07 Å
NMR ensemble rmsDistance rms dev: 0.09 Å

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