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- PDB-1j6y: Solution structure of Pin1At from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 1j6y
TitleSolution structure of Pin1At from Arabidopsis thaliana
Componentspeptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / prolyl cis/trans isomerase / parvulin / PIN1 / phosphorylation
Function / homology
Function and homology information


regulation of flower development / gravitropism / plasmodesma / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / regulation of protein localization / regulation of cell cycle / endoplasmic reticulum / mitochondrion / nucleus ...regulation of flower development / gravitropism / plasmodesma / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / regulation of protein localization / regulation of cell cycle / endoplasmic reticulum / mitochondrion / nucleus / plasma membrane / cytosol
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase Pin1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsLandrieu, I. / Wieruszeski, J.M. / Wintjens, R. / Inze, D. / Lippens, G.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Solution Structure of the Single-domain Prolyl Cis/Trans Isomerase PIN1At from Arabidopsis thaliana
Authors: Landrieu, I. / Wieruszeski, J.M. / Wintjens, R. / Inze, D. / Lippens, G.
#1: Journal: J.Biomol.NMR / Year: 2000
Title: Letter to the editor : sequence-specific 1H, 13C and 15N chemical shift backbone NMR assigment and secondary structure of the Arabidopsis thaliana PIN1At protein
Authors: Landrieu, I. / Wieruszeski, J.M. / Odaert, B. / Inze, D. / Grzesiek, S. / Lippens, G.
#2: Journal: J.Biol.Chem. / Year: 2000
Title: The Arabidopsis thaliana PIN1At gene encodes a single-domain phosphorylation-dependent peptidyl prolyl cis/trans isomerase
Authors: Landrieu, I. / De Veylder, L. / Fruchart, J.-S. / Odaert, B. / Casteels, P. / Portetelle, D. / Van Montagu, M. / Inze, D. / Lippens, G.
History
DepositionMay 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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


Theoretical massNumber of molelcules
Total (without water)15,2091
Polymers15,2091
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 / 150structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein peptidyl-prolyl cis-trans isomerase


Mass: 15209.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9SL42

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 15N-separated NOESY
1323D 15N-SEPARATED TOCSY
1423D HBHA(CO)NH
1533D CBCANH
1633D CBCA(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM PIN1At 50 mM deuterated Tris-HCl pH6.3 100 mM NaCl 1 mM dithiothreitol 1mM phenylmethylsulfonyl fluoride 0.5 mM EDTA90% H2O/10% D2O
20.7 mM PIN1At U-15N50 mM deuterated Tris-HCl pH6.3 100 mM NaCl 1 mM dithiothreitol 1mM phenylmethylsulfonyl fluoride 0.5 mM EDTA90% H2O/10% D2O
30.7 mM PIN1At U-15N,13C 50 mM deuterated Tris-HCl pH6.3 100 mM NaCl 1 mM dithiothreitol 1mM phenylmethylsulfonyl fluoride 0.5 mM EDTA90% H2O/10% D2O
40.7 mM PIN1At U-13C 50 mM deuterated Tris-HCl pH6.3 100 mM NaCl 1 mM dithiothreitol 1mM phenylmethylsulfonyl fluoride 0.5 mM EDTA100% D2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 6.3 / Pressure: ambient / Temperature: 293 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 spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGER,A.T.structure solution
SNARF0.8.9VAN HOESEL, F.data analysis
X-PLOR3.851BRUNGER,A.T.refinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 20

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