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- PDB-2lme: Solid-state NMR structure of the membrane anchor domain of the tr... -

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Basic information

Entry
Database: PDB / ID: 2lme
TitleSolid-state NMR structure of the membrane anchor domain of the trimeric autotransporter YadA
ComponentsAdhesin yadA
KeywordsCELL ADHESION / TRIMERIC AUTOTRANSPORTER / MEMBRANE PROTEIN
Function / homology
Function and homology information


collagen binding / cell outer membrane / protein transport / cell adhesion / cell surface
Similarity search - Function
Outer membrane adhesion, Yersinia / GSPII I/J protein-like / Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Pilin-like ...Outer membrane adhesion, Yersinia / GSPII I/J protein-like / Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Pilin-like / Serralysin-like metalloprotease, C-terminal / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesYersinia enterocolitica subsp. enterocolitica (bacteria)
MethodSOLID-STATE NMR / molecular dynamics
Model detailsclosest to the average, model 7
AuthorsShahid, S.A. / Bardiaux, B. / Franks, W.T. / Habeck, M. / Linke, D. / van Rossum, B.
CitationJournal: Nat.Methods / Year: 2012
Title: Membrane-protein structure determination by solid-state NMR spectroscopy of microcrystals.
Authors: Shahid, S.A. / Bardiaux, B. / Franks, W.T. / Krabben, L. / Habeck, M. / van Rossum, B.J. / Linke, D.
History
DepositionNov 30, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: 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
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: Adhesin yadA
B: Adhesin yadA
C: Adhesin yadA


Theoretical massNumber of molelcules
Total (without water)33,8653
Polymers33,8653
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 / 400Highest posterior probability
RepresentativeModel #1closest to the average

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Components

#1: Protein Adhesin yadA


Mass: 11288.466 Da / Num. of mol.: 3 / Fragment: Outer membrane region, residues 333-422
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica subsp. enterocolitica (bacteria)
Strain: 8081 / Gene: yadA, YEP0066 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 omp8 / References: UniProt: A1JUB7

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 13C-13C DARR 25 ms
1212D 13C-13C DARR 50 ms
1312D 13C-13C DARR 100 ms
1412D 13C-13C DARR-CP- 15 ms
1512D 13C-13C DARR-CP- 40 ms
1612D 13C-13C DARR-CP- 70 ms
1712D 13C-13C PDSD 15 ms
1812D 13C-13C PDSD 100 ms
1912D 1H-13C INEPT
11012D 13C-13C DREAM 1.5 ms
11112D 13C-13C DREAM AB
11212D 13C-13C DREAM BG
11312D 13C-13C Me-only 70 ms
11412D 13C-13C REDOR 1 ms
11512D 15N-13C NCA
11612D 15N-13C NCO
11712D NCACX
11812D NCOCX
11913D NCACX 25 ms
12013D NCOCX 25 ms
12113D NCACX 100 ms
12213D NCACX 200 ms
12313D NCOCX 200 ms
12413D NCACX 500 ms
12513D NCACB 3 ms
12612D 13C-13C DARR
12712D 13C-13C CPPI-DARR-DD
12812D 13C-13C CPPI-DARR
12912D 13C-13C PDSD
13012D 13C-13C PAR
13112D 15N-13C TEDOR
13212D 13C-13C CHHC
13312D 15N-13C NHHC

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Sample preparation

DetailsContents: 11.5 M [U-13C; U-15N] YadA membrane anchor domain
SampleConc.: 11.5 M / Component: YadA membrane anchor domain-1 / Isotopic labeling: [U-13C; U-15N]
Sample conditionspH: 7 / Pressure: ambient / Temperature: 275 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE9003
Bruker AvanceBrukerAVANCE8504

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.113Goddardchemical shift assignment
TALOS+Cornilescu, Delaglio and Baxdata analysis
ISDRieping, Habeck and Nilgesrefinement
ISDRieping, Habeck and Nilgesstructure solution
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: Structures were determined using a combination of replica-exchange Monte Carlo and bayesian inference using the Inferential Structure Determination program (ISD)
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: Highest posterior probability / Conformers calculated total number: 400 / Conformers submitted total number: 20

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