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- PDB-1qnh: Plasmodium falciparum Cyclophilin (double mutant) complexed with ... -

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Basic information

Entry
Database: PDB / ID: 1qnh
TitlePlasmodium falciparum Cyclophilin (double mutant) complexed 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


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / intracellular membrane-bounded organelle / plasma membrane / cytosol
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 speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
TOLYPOCLADIUM INFLATUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPeterson, M.R. / Hall, D.R. / Hunter, W.N.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: The Three-Dimensional Structure of a Plasmodium Falciparum Cyclophilin in Complex with the Potent Anti-Malarial Cyclosporin A
Authors: Peterson, M.R. / Hall, D.R. / Berriman, M. / Leonard, G.A. / Fairlamb, A.H. / Hunter, W.N.
#1: Journal: Biochem.J. / Year: 1998
Title: Detailed Characterization of a Cyclophilin from the Human Malaria Parasite Plasmodium Falciparum
Authors: Berriman, M. / Fairlamb, A.H.
History
DepositionOct 14, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2000Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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)40,2104
Polymers40,2104
Non-polymers00
Water3,837213
1
A: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
C: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)20,1052
Polymers20,1052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-8.2 kcal/mol
Surface area9520 Å2
MethodPQS
2
B: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
D: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)20,1052
Polymers20,1052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-8.4 kcal/mol
Surface area9470 Å2
MethodPQS
Unit cell
Length a, b, c (Å)92.110, 115.120, 39.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.16335, -0.98606, 0.03182), (0.96489, -0.1664, -0.20321), (0.20567, -0.0025, 0.97862)
Vector: 63.67295, 72.66035, 11.18299)

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Components

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


Mass: 18884.408 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q25756, peptidylprolyl isomerase
#2: Protein/peptide CYCLOSPORIN A / CYCLOSPORINE / 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.: 213 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. HERE, CYCLOSPORIN A IS REPRESENTED BY THE SEQUENCE (SEQRES) ...CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. HERE, CYCLOSPORIN A IS REPRESENTED BY THE SEQUENCE (SEQRES) GROUP: 1 NAME: CYCLOSPORIN A CHAIN: C, D COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 11 DESCRIPTION: CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55 %
Crystal growpH: 7.7 / Details: pH 7.70
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein/drug complex1drop
235 mMHEPES1drop
315 %(w/v)PEG15001drop
430 %(w/v)PEG15001reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98
DetectorType: FUJI BAS-2000 IMAGE PLATE / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→24 Å / Num. obs: 24606 / % possible obs: 98.2 % / Redundancy: 5 % / Biso Wilson estimate: 34.2 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 17.8
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 3.7 / % possible all: 92.7

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CWA

1cwa


Resolution: 2.1→24 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: REFINEMENT AT EARLY STAGES UTILISED X-PLOR AND REFMAC AND NCS RESTRAINTS WERE RELEASED AT THE FINAL STAGES OF REFINEMENT THE SIDE CHAINS OF THE FOLLOWING RESIDUES ARE DISORDERED ASN A 15, ...Details: REFINEMENT AT EARLY STAGES UTILISED X-PLOR AND REFMAC AND NCS RESTRAINTS WERE RELEASED AT THE FINAL STAGES OF REFINEMENT THE SIDE CHAINS OF THE FOLLOWING RESIDUES ARE DISORDERED ASN A 15, LYS A 51, LYS A 155, ARG B 49, LYS B 51, ARG B 88, LYS B 155, LYS B 160 SER A 2 IS DISORDERED AND NOT OBSERVED
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2471 10 %RANDOM
Rwork0.17 ---
obs0.17 24606 98.2 %-
Displacement parametersBiso mean: 26.6 Å2
Refinement stepCycle: LAST / Resolution: 2.1→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2775 0 0 213 2988
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.9171.5
X-RAY DIFFRACTIONc_mcangle_it1.3452
X-RAY DIFFRACTIONc_scbond_it1.5482
X-RAY DIFFRACTIONc_scangle_it2.0212.5
LS refinement shellResolution: 2.1→2.11 Å / Total num. of bins used: 49
RfactorNum. reflection% reflection
Rfree0.242 53 10 %
Rwork0.227 390 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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