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- PDB-2rqs: 3D structure of Pin from the psychrophilic archeon Cenarcheaum sy... -

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Basic information

Entry
Database: PDB / ID: 2rqs
Title3D structure of Pin from the psychrophilic archeon Cenarcheaum symbiosum (CsPin)
ComponentsParvulin-like peptidyl-prolyl isomerase
KeywordsISOMERASE / cis/trans isomerisation / Cenarcheaum symbiosum / low temperature / NIMA-kinase / parvulin / Pin1 / cell cycle
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / rRNA processing / DNA binding
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase PIN4 / PPIC-type PPIASE domain / 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
peptidylprolyl isomerase
Similarity search - Component
Biological speciesCenarchaeum symbiosum (archaea)
MethodSOLUTION NMR / simulated annealing
Model detailsPin (protein interacting with NIMA-kinase) catalyzes the cis/trans isomerisation of Xaa-Pro peptide ...Pin (protein interacting with NIMA-kinase) catalyzes the cis/trans isomerisation of Xaa-Pro peptide bonds of target proteins.
AuthorsZhukov, I. / Jaremko, L. / Jaremko, M. / Mueller, J.W. / Bayer, P.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure and Dynamics of the First Archaeal Parvulin Reveal a New Functionally Important Loop in Parvulin-type Prolyl Isomerases
Authors: Jaremko, L. / Jaremko, M. / Elfaki, I. / Mueller, J.W. / Ejchart, A. / Bayer, P. / Zhukov, I.
History
DepositionNov 17, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Parvulin-like peptidyl-prolyl isomerase


Theoretical massNumber of molelcules
Total (without water)10,5161
Polymers10,5161
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Parvulin-like peptidyl-prolyl isomerase / CsPin / Peptidyl-prolyl cis/trans isomerase


Mass: 10516.255 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cenarchaeum symbiosum (archaea) / Gene: pinA / Production host: Escherichia coli (E. coli) / References: UniProt: O74049, peptidylprolyl isomerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Pin (protein interacting with NIMA-kinase) catalyzes the cis/trans isomerisation of Xaa-Pro peptide bonds of target proteins.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H TOCSY
1413D CBCA(CO)NH
1513D C(CO)NH
1613D HNCO
1713D HNCA
1813D HN(CA)CB
1913D HBHA(CO)NH
11013D 1H-13C NOESY
11113D 1H-15N NOESY

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Sample preparation

DetailsContents: 0.6mM [U-100% 13C; U-100% 15N] CsPin, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.6 mM / Component: CsPin / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.1 / pH: 7.5 / Pressure: ambient / Temperature: 289 K

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NMR measurement

NMR spectrometerType: Varian Uniform NMR System / Manufacturer: Varian / Model: Uniform NMR System / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1585 / Hydrogen bond constraints total count: 76
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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