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- PDB-2m2a: NMR solution structure of the two domain PPIase SlpA from Escheri... -

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Basic information

Entry
Database: PDB / ID: 2m2a
TitleNMR solution structure of the two domain PPIase SlpA from Escherichia coli
ComponentsFKBP-type 16 kDa peptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / FKBP fold
Function / homology
Function and homology information


chaperone-mediated protein folding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cytosol
Similarity search - Function
Thrombin, subunit H - #330 / : / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Thrombin, subunit H / Roll ...Thrombin, subunit H - #330 / : / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Thrombin, subunit H / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FKBP-type 16 kDa peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsKovermann, M. / Weininger, U. / Balbach, J.
CitationJournal: To be Published
Title: NMR solution structure of the two domain PPIase SlpA from Escherichia coli
Authors: Kovermann, M. / Geitner, A. / Weininger, U. / Schmid, F. / Balbach, J.
History
DepositionDec 17, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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
Revision 1.2May 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: FKBP-type 16 kDa peptidyl-prolyl cis-trans isomerase


Theoretical massNumber of molelcules
Total (without water)16,0231
Polymers16,0231
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)10 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein FKBP-type 16 kDa peptidyl-prolyl cis-trans isomerase / PPIase / Rotamase


Mass: 16022.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0AEM0, peptidylprolyl isomerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D 1H-13C NOESY aliphatic
1513D 1H-13C NOESY aromatic
1613D 1H-15N NOESY
1713D HNCA
1813D HN(CA)CB
1913D HN(COCA)CB
11013D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 1 mM [U-99% 13C; U-99% 15N] SlpA, 100 mM potassium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMSlpA-1[U-99% 13C; U-99% 15N]1
100 mMpotassium phosphate-21
Sample conditionsIonic strength: 0.1 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.3Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificpeak picking
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 10

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