3RFY Isomerase date Apr 07, 2011
title Crystal Structure Of Arabidopsis Thaliana Cyclophilin 38 (At
authors D.Vasudevan, K.Swaminathan
compound source
Molecule: Peptidyl-Prolyl Cis-Trans Isomerase Cyp38, Chloro
Chain: A
Synonym: Ppiase Cyp38, Rotamase Cyp38, Thylakoid Lumen Ppia
Ec: 5.2.1.8
Engineered: Yes
Organism_scientific: Arabidopsis Thaliana
Organism_common: Mouse-Ear Cress,Thale-Cress
Organism_taxid: 3702
Gene: At3g01480, Cyp38, F4p13.3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-Kg
symmetry Space Group: C 2 2 21
R_factor 0.248 R_Free 0.266
crystal
cell
length a length b length c angle alpha angle beta angle gamma
57.690 96.720 166.820 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.39 Å
ligand
enzyme Isomerase E.C.5.2.1.8 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of Arabidopsis cyclophilin38 reveals a previously uncharacterized immunophilin fold and a possible autoinhibitory mechanism., Vasudevan D, Fu A, Luan S, Swaminathan K, Plant Cell. 2012 Jun;24(6):2666-74. doi: 10.1105/tpc.111.093781. Epub 2012 Jun, 15. PMID:22706283
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (64 Kb) [Save to disk]
  • Biological Unit Coordinates (3rfy.pdb1.gz) 58 Kb
  • Biological Unit Coordinates (3rfy.pdb2.gz) 115 Kb
  • CSU: Contacts of Structural Units for 3RFY
  • Structure Factors (129 Kb)
  • Retrieve 3RFY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3RFY from S2C, [Save to disk]
  • Re-refined 3rfy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3RFY in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3RFY
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3RFY, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3rfy_A] [3rfy]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3RFY
  • Community annotation for 3RFY at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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