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- PDB-1jnt: NMR Structure of the E. coli Peptidyl-Prolyl cis/trans-Isomerase ... -

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Basic information

Entry
Database: PDB / ID: 1jnt
TitleNMR Structure of the E. coli Peptidyl-Prolyl cis/trans-Isomerase Parvulin 10
ComponentsPEPTIDYL-PROLYL CIS-TRANS ISOMERASE C
KeywordsISOMERASE / ALPHA-BETA SANDWICH / CIS PEPTIDE BOND
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cytoplasm
Similarity search - Function
: / PPIC-type PPIASE domain / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase C
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / The averaged structure of the ensemble (1JNS) was regularized under experimental constraints
Model type detailsminimized average
AuthorsKuehlewein, A. / Voll, G. / Schelbert, B. / Kessler, H. / Fischer, G. / Rahfeld, J.U. / Gemmecker, G.
CitationJournal: Protein Sci. / Year: 2004
Title: Solution structure of Escherichia coli Par10: The prototypic member of the Parvulin family of peptidyl-prolyl cis/trans isomerases.
Authors: Kuehlewein, A. / Voll, G. / Alvarez, B.H. / Kessler, H. / Fischer, G. / Rahfeld, J.U. / Gemmecker, G.
History
DepositionJul 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE C


Theoretical massNumber of molelcules
Total (without water)10,1181
Polymers10,1181
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)1 / -
Representativeminimized average structure

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Components

#1: Protein PEPTIDYL-PROLYL CIS-TRANS ISOMERASE C / PARVULIN / PPIASE C / ROTAMASE C


Mass: 10117.838 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: parA / Plasmid: pSEP612 / Production host: Escherichia coli (E. coli) / Strain (production host): M15[pREP4] / References: UniProt: P0A9L5, peptidylprolyl isomerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNHA
1213D 15N-separated NOESY
1323D 13C-separated NOESY
1423D 13C/13C-separated NOESY
1523D 13C/15N-separated NOESY
1622D MEXICO
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-15N] Parvulin 10, 10 mM phosphate buffer, pH 6.0, 100 mM KCl, 1 mM EDTA, 1 mM DTE90% H2O/10% D2O
20.8 mM [U-13C, 15N] Parvulin 10, 10 mM phosphate buffer, pH 6.0, 100 mM KCl, 1 mM EDTA, 1 mM DTE90% H2O/10% D2O
Sample conditionsIonic strength: 100 mM KCl / pH: 6 / Pressure: ambient / Temperature: 297.6 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX7502

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6BRUKER, KARLSRUHEcollection
XwinNMR2.6BRUKER, KARLSRUHEprocessing
TRIAD6.6TRIPOS, ST. LOUISdata analysis
ARIA0.53NILGES ET AL.structure solution
CNS0.5BRUNGER ET AL.structure solution
X-PLOR3.851BRUNGER ET AL.structure solution
X-PLOR3.851BRUNGERrefinement
RefinementMethod: The averaged structure of the ensemble (1JNS) was regularized under experimental constraints
Software ordinal: 1
Details: the structures are based on 1097 NOE-derived distance constraints, 68 dihedral restraints for CSI-derived helical regions, 42 3J(HN,HA) restraints, 30 distance constraints for hydrogen bonds ...Details: the structures are based on 1097 NOE-derived distance constraints, 68 dihedral restraints for CSI-derived helical regions, 42 3J(HN,HA) restraints, 30 distance constraints for hydrogen bonds based on CSI and MEXICO data.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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