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- PDB-2rs4: NMR structure of stereo-array isotope labelled (SAIL) peptidyl-pr... -

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Basic information

Entry
Database: PDB / ID: 2rs4
TitleNMR structure of stereo-array isotope labelled (SAIL) peptidyl-prolyl cis-trans isomerase from E. coli (EPPIb)
ComponentsPeptidyl-prolyl cis-trans isomerase B
KeywordsISOMERASE / SAIL
Function / homology
Function and homology information


chaperone-mediated protein folding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cytosol
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase, E. coli cyclophilin A-like / Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily ...Cyclophilin-type peptidyl-prolyl cis-trans isomerase, E. coli cyclophilin A-like / Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model 1
AuthorsTakeda, M. / Jee, J. / Ono, A.M. / Okuma, K. / Terauchi, T. / Kainosho, M.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Hydrogen exchange study on the hydroxyl groups of serine and threonine residues in proteins and structure refinement using NOE restraints with polar side-chain groups
Authors: Takeda, M. / Jee, J. / Ono, A.M. / Terauchi, T. / Kainosho, M.
History
DepositionJul 16, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Dec 21, 2016Group: Structure summary
Revision 1.3Jun 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 1.4May 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: Peptidyl-prolyl cis-trans isomerase B


Theoretical massNumber of molelcules
Total (without water)18,1741
Polymers18,1741
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 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase B / PPIase B / Rotamase B


Mass: 18174.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ppiB, b0525, JW0514 / Production host: Escherichia coli (E. coli) / References: UniProt: P23869, 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 HNCA
1513D HN(CA)CB
1613D HNCO
1713D CBCA(CO)NH
1813D HN(CO)CA
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY aliphatic
11213D 1H-13C NOESY aromatic
11323D 1H-13C NOESY aromatic
11433D 1H-13C NOESY aromatic
11512D HB(CBCG)HE
11622D HB(CBCGCZ) HZ

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM SAIL [e-SAIL Phe, e-SAIL Tyr] EPPIb-1, 50 mM sodium phosphate-2, 1 mM DTT-3, 100 mM sodium chloride-4, 90% H2O/10% D2O90% H2O/10% D2O
20.3 mM SAIL [z-SAIL Phe, e-SAIL Tyr] EPPIb-5, 50 mM sodium phosphate-6, 1 mM DTT-7, 100 mM sodium chloride-8, 90% H2O/10% D2O90% H2O/10% D2O
30.3 mM SAIL [d-SAIL Phe, d-SAIL Tyr] EPPIb-9, 50 mM sodium phosphate-10, 1 mM DTT-11, 100 mM sodium chloride-12, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMEPPIb-1SAIL [e-SAIL Phe, e-SAIL Tyr]1
50 mMsodium phosphate-21
1 mMDTT-31
100 mMsodium chloride-41
0.3 mMEPPIb-5SAIL [z-SAIL Phe, e-SAIL Tyr]2
50 mMsodium phosphate-62
1 mMDTT-72
100 mMsodium chloride-82
0.3 mMEPPIb-9SAIL [d-SAIL Phe, d-SAIL Tyr]3
50 mMsodium phosphate-103
1 mMDTT-113
100 mMsodium chloride-123
Sample conditionsIonic strength: 0.4 / pH: 6.2 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker DRXBrukerDRX8002

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Processing

NMR softwareName: Amber
Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm
Classification: refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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