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- PDB-2poy: Cryptosporidium parvum cyclophilin type peptidyl-prolyl cis-trans... -

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Basic information

Entry
Database: PDB / ID: 2poy
TitleCryptosporidium parvum cyclophilin type peptidyl-prolyl cis-trans isomerase cgd2_4120 in complex with cyclosporin A
Components
  • CYCLOSPORIN A
  • PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
KeywordsISOMERASE/IMMUNOSUPPRESSANT / ISOMERASE-IMMUNOSUPPRESSANT COMPLEX / CYCLOPHILIN-CYCLOSPORIN COMPLEX / CYCLOSPORIN A / IMMUNOSUPPRESSANT / CYCLOPHILIN / ISOMERASE / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding
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
Cyclosporin A / : / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesCRYPTOSPORIDIUM PARVUM IOWA II (eukaryote)
TOLYPOCLADIUM INFLATUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWernimont, A.K. / Lew, J. / Hills, T. / Kozieradzki, I. / Lin, Y.H. / Hassanali, A. / Zhao, Y. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. ...Wernimont, A.K. / Lew, J. / Hills, T. / Kozieradzki, I. / Lin, Y.H. / Hassanali, A. / Zhao, Y. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R. / Artz, J.D. / Xiao, T. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Cryptosporidium Parvum Cyclophilin Type Peptidyl-Prolyl Cis-Trans Isomerase Cgd2_4120 in Complex with Cyclosporin A.
Authors: Wernimont, A.K. / Lew, J. / Hills, T. / Kozieradzki, I. / Lin, Y.H. / Hassanali, A. / Zhao, Y. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. ...Authors: Wernimont, A.K. / Lew, J. / Hills, T. / Kozieradzki, I. / Lin, Y.H. / Hassanali, A. / Zhao, Y. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R. / Artz, J.D. / Xiao, T.
History
DepositionApr 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Nov 1, 2017Group: Advisory / Derived calculations
Category: pdbx_struct_assembly / pdbx_validate_polymer_linkage
Item: _pdbx_struct_assembly.method_details
Revision 1.6Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.7Nov 15, 2023Group: Advisory / Data collection / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_validate_polymer_linkage / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
B: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
C: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
T: CYCLOSPORIN A
U: CYCLOSPORIN A
V: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)64,6646
Polymers64,6646
Non-polymers00
Water5,675315
1
A: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
T: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)21,5552
Polymers21,5552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-7 kcal/mol
Surface area7820 Å2
MethodPISA
2
B: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
U: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)21,5552
Polymers21,5552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-7 kcal/mol
Surface area8100 Å2
MethodPISA
3
C: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
V: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)21,5552
Polymers21,5552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-8 kcal/mol
Surface area7800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.482, 119.303, 127.877
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PEPTIDYL-PROLYL CIS-TRANS ISOMERASE


Mass: 20334.020 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CRYPTOSPORIDIUM PARVUM IOWA II (eukaryote)
Strain: IOWA TYPE II / Gene: CGD2_4120 / Plasmid: P15_TEV/LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH5A / References: UniProt: A3FQA7
#2: Protein/peptide CYCLOSPORIN A / CICLOSPORIN / CICLOSPORINE


Type: Cyclic peptide / Class: Immunosuppressant / Mass: 1220.625 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI.
Source: (synth.) TOLYPOCLADIUM INFLATUM (fungus) / References: NOR: NOR00033, Cyclosporin A
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. HERE, CYCLOSPORIN A IS REPRESENTED BY THE SEQUENCE (SEQRES)
Sequence detailsTHE N-TERMINAL 18 RESIDUES 'MHHHHHHSSGREDLYFNG' IN CHAINS A, B AND C IS AN ENGINEERED EXPRESSION TAG

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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: 2.15 Å3/Da / Density % sol: 42.81 %
Crystal growpH: 3.5
Details: 25 % PEG 3350, 0.1 M CITRIC ACID PH 3.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9177
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9177 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 51177 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.103 / Rsym value: 0.083 / Net I/σ(I): 6.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.312 / % possible all: 78.8

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å43.62 Å
Translation2.5 Å43.62 Å

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PLU

2plu


Resolution: 1.8→34.88 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.868 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2598 5.1 %RANDOM
Rwork0.193 ---
obs0.195 51164 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4096 0 0 315 4411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224185
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.9825662
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4525514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32724.417163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48615636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4331513
X-RAY DIFFRACTIONr_chiral_restr0.1040.2623
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023205
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.22199
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.22932
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2319
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9161.52745
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.47224307
X-RAY DIFFRACTIONr_scbond_it2.22531616
X-RAY DIFFRACTIONr_scangle_it3.364.51355
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 142 -
Rwork0.262 2700 -
obs--74.63 %

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