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- PDB-2kxx: NMR Structure of Escherichia coli BamE, a Lipoprotein Component o... -

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Basic information

Entry
Database: PDB / ID: 2kxx
TitleNMR Structure of Escherichia coli BamE, a Lipoprotein Component of the beta-Barrel Assembly Machinery Complex
ComponentsSmall protein A
KeywordsPROTEIN BINDING / E coli protein / lipoprotein
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / protein-macromolecule adaptor activity / response to antibiotic / membrane / identical protein binding
Similarity search - Function
Beta-lactamase Inhibitory Protein; Chain:B, domain 1 / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 - #10 / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA / SmpA / OmlA family / BamE-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Outer membrane protein assembly factor BamE
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsKim, K. / Okon, M. / Escobar, E. / Kang, H. / McIntosh, L. / Paetzel, M.
CitationJournal: Biochemistry / Year: 2011
Title: Structural Characterization of Escherichia coli BamE, a Lipoprotein Component of the beta-Barrel Assembly Machinery Complex.
Authors: Kim, K.H. / Kang, H.S. / Okon, M. / Escobar-Cabrera, E. / McIntosh, L.P. / Paetzel, M.
History
DepositionMay 13, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Jun 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 1.4May 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: Small protein A


Theoretical massNumber of molelcules
Total (without water)10,7021
Polymers10,7021
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 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Small protein A


Mass: 10701.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: b2617, JW2598, smpA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A937

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: First four residues (GSHM) are remainter of thrombin-cleaved 6-His tag.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D 1H-15N NOESY
1413D HNCO
1513D HN(CA)CB
1613D HN(CO)CA
1713D 1H-13C NOESY
1812D 1H-1H COSY

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Sample preparation

DetailsContents: 0.5 mM [U-100% 13C; U-100% 15N] E. coli protein, 15 % D2O, 85 % H2O, 20 mM Na2HPO4/NaH2PO4, 85% H2O/15% D2O
Solvent system: 85% H2O/15% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mME. coli protein-1[U-100% 13C; U-100% 15N]1
15 %D2O-21
85 %H2O-31
20 mMNa2HPO4/NaH2PO4-41
Sample conditionsIonic strength: 0.02 / pH: 6.6 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Varian Unity / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Sparky3.113Goddardchemical shift assignment
Sparky3.113Goddardpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
ARIA2Rieping, Habeck, Bardiaux, Bernard, Malliavin and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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