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- PDB-3eov: Crystal structure of cyclophilin from Leishmania donovani ligated... -

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Basic information

Entry
Database: PDB / ID: 3eov
TitleCrystal structure of cyclophilin from Leishmania donovani ligated with cyclosporin A
Components
  • CYCLOSPORIN A
  • PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
KeywordsISOMERASE/IMMUNOSUPPRESSANT / ISOMERASE-IMMUNOSUPPRESSANT COMPLEX / CYCLOPHILIN-CYCLOSPORIN COMPLEX / CYCLOSPORIN A / IMMUNOSUPPRESSANT / CYCLOPHILIN
Function / homology
Function and homology information


cyclosporin A binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / intracellular membrane-bounded organelle / 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
Cyclosporin A / : / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesLEISHMANIA DONOVANI (eukaryote)
TOLYPOCLADIUM INFLATUM (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsVenugopal, V. / Dasgupta, D. / Datta, A.K. / Banerjee, R.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of Cyclophilin from Leishmania Donovani Bound to Cyclosporin at 2.6 A Resolution: Correlation between Structure and Thermodynamic Data.
Authors: Venugopal, V. / Datta, A.K. / Bhattacharyya, D. / Dasgupta, D. / Banerjee, R.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Structure of Cyclophilin from Leishmania Donovani at 1.97 A Resolution.
Authors: Venugopal, V. / Sen, B. / Datta, A.K. / Banerjee, R.
#2: Journal: J.Biol.Chem. / Year: 2001
Title: Lack of Abundance of Cytoplasmic Cyclosporin A- Binding Protein Renders Free-Living Leishmania Donovani Resistant to Cyclosporin A.
Authors: Dutta, M. / Delhi, P. / Sinha, K.M. / Banerjee, R. / Datta, A.K.
History
DepositionSep 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: 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 1.5Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.6Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / 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

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Assembly

Deposited unit
A: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
B: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
C: CYCLOSPORIN A
D: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)40,6224
Polymers40,6224
Non-polymers00
Water1,36976
1
A: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
C: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)20,3112
Polymers20,3112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-7.6 kcal/mol
Surface area7930 Å2
MethodPISA
2
B: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
D: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)20,3112
Polymers20,3112
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-7.6 kcal/mol
Surface area8020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.810, 83.125, 73.580
Angle α, β, γ (deg.)90.00, 103.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 19090.541 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA DONOVANI (eukaryote) / Gene: CYP / Plasmid: PQE32 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: Q9U9R3, peptidylprolyl isomerase
#2: Protein/peptide CYCLOSPORIN A / CICLOSPORIN / CICLOSPORINE


Type: Cyclic peptide / Class: Immunosuppressant / Mass: 1220.625 Da / Num. of mol.: 2 / 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.: 76 / 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 5 RESIDUES 'HHHHHH' IN CHAINS A AND B 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: 2.57 Å3/Da / Density % sol: 52.22 %
Crystal growpH: 8.5
Details: 0.02M TRIS, 15% PEG3350, 0.1M NACL, 0.02% AZIDE, PH 8.5, 6% ETHYL ALCOHOL, CONCENTRATION: 10 MG/ML 1:1 CYCLOPHILIN-CYCLOSPORIN COMPLEX, TEMPERATURE 292K, BATCH METHOD, PH 8.50, SMALL TUBES

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2008 / Details: OSMIC MAXFLUX CONFOCAL MULTILAY
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 12040 / % possible obs: 95.3 % / Observed criterion σ(I): 2 / Redundancy: 4.11 % / Biso Wilson estimate: 52.4 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 2.6 / % possible all: 96.5

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HAQ

2haq


Resolution: 2.6→27.48 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 780102.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.251 623 5.2 %RANDOM
Rwork0.207 ---
obs0.207 12040 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.6 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 49.6 Å2
Baniso -1Baniso -2Baniso -3
1-12.41 Å20 Å21.4 Å2
2--2.4 Å20 Å2
3----14.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.6→27.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2728 0 0 76 2804
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.149 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.211 2 0.1 %
Rwork0.315 1968 -
obs--94.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CSA.PARAMCSA.TOP

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