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- PDB-1e8k: Cyclophilin 3 Complexed With Dipeptide Ala-Pro -

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Basic information

Entry
Database: PDB / ID: 1e8k
TitleCyclophilin 3 Complexed With Dipeptide Ala-Pro
ComponentsPEPTIDYL-PROLYL CIS-TRANS ISOMERASE 3
KeywordsISOMERASE
Function / homology
Function and homology information


cyclosporin A binding / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidyl-prolyl cis-trans isomerase activity / peptidylprolyl isomerase / protein folding / mitochondrion / nucleus / cytoplasm
Similarity search - Function
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
ALANINE / PROLINE / Peptidyl-prolyl cis-trans isomerase 3
Similarity search - Component
Biological speciesCAENORHABDITIS ELEGANS (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWu, S.Y. / Dornan, J. / Kontopidis, G. / Taylor, P. / Walkinshaw, M.D.
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2001
Title: The First Direct Determination of a Ligand Binding Constant in Protein Crystals
Authors: Wu Sy, S.Y. / Dornan, J. / Kontopidis, G. / Taylor, P. / Walkinshaw, M.D.
#1: Journal: J.Biol.Chem. / Year: 1999
Title: Biochemical and Structural Characterization Ivergent Loop Cyclophilin from Caenorhabditis Elegans of A
Authors: Dornan, J. / Page, A.P. / Taylor, P. / Wu, S.Y. / Winter, A.D. / Husi, H. / Walkinshawr, M.D.
History
DepositionSep 25, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2001Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jul 24, 2013Group: Derived calculations / Other
Revision 1.3Jun 20, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_unobs_or_zero_occ_atoms / struct_conn
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7803
Polymers18,5761
Non-polymers2042
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.035, 61.035, 122.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2041-

HOH

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Components

#1: Protein PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 3 / PPIASE 3 / CYCLOPHILIN-3 / ROTAMASE 3


Mass: 18576.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAENORHABDITIS ELEGANS (invertebrata) / Plasmid: PET-5A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P52011, peptidylprolyl isomerase
#2: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#3: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 59.73 %
Crystal growpH: 5.6 / Details: MPEG5000, SODIUM CITRATE, PH 5.6
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop / Details: Dornan, J., (1999) J.Biol.Chem., 274, 34877.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.5 mg/mlprotein1drop
250 mMsodium citrate1drop
329-31 %(w/v)mPEG50001drop
4100 mMsodium citrate1reservoir
531 %mPEG50001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 19230 / % possible obs: 97.6 % / Redundancy: 7.92 % / Rsym value: 0.079 / Net I/σ(I): 12.85
Reflection shellResolution: 1.9→1.93 Å / Mean I/σ(I) obs: 2.13 / Rsym value: 0.332 / % possible all: 88.2
Reflection
*PLUS
Num. measured all: 152448 / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
Rmerge(I) obs: 0.332

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DYW

1dyw


Resolution: 1.9→10 Å / Num. parameters: 6247 / Num. restraintsaints: 5392 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2505 934 5 %RANDOM
obs0.1826 -93.4 %-
all-17589 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1497.31
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1297 0 13 229 1539
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.023
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0.008
X-RAY DIFFRACTIONs_from_restr_planes0.0278
X-RAY DIFFRACTIONs_zero_chiral_vol0.038
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.049
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.148
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.086
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rwork: 0.1826
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_bond_d / Dev ideal: 0.03

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