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- PDB-8b58: Crystal Structure of Cyclophilin TgCyp23 from Toxoplasma gondii i... -

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Basic information

Entry
Database: PDB / ID: 8b58
TitleCrystal Structure of Cyclophilin TgCyp23 from Toxoplasma gondii in complex with Cyclosporin A
Components
  • Cyclosporin A
  • Peptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / CYCLOPHILIN / ISOMERASE-IMMUNOSUPPRESSANT COMPLEX
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, 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 speciesToxoplasma gondii (eukaryote)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.1 Å
AuthorsJimenez-Faraco, E. / Hermoso, J.A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)PID2020-115331GB-I00 Spain
CitationJournal: Acs Infect Dis. / Year: 2023
Title: Structural Basis for Cyclosporin Isoform-Specific Inhibition of Cyclophilins from Toxoplasma gondii .
Authors: Favretto, F. / Jimenez-Faraco, E. / Conter, C. / Dominici, P. / Hermoso, J.A. / Astegno, A.
History
DepositionSep 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

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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)48,4384
Polymers48,4384
Non-polymers00
Water8,431468
1
A: Peptidyl-prolyl cis-trans isomerase
C: Cyclosporin A


Theoretical massNumber of molelcules
Total (without water)24,2192
Polymers24,2192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-8 kcal/mol
Surface area9180 Å2
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase
D: Cyclosporin A


Theoretical massNumber of molelcules
Total (without water)24,2192
Polymers24,2192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-8 kcal/mol
Surface area9150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.400, 119.424, 46.350
Angle α, β, γ (deg.)90.00, 103.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase / PPIase


Mass: 22998.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGRH88_026260 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7J6KAD1, peptidylprolyl isomerase
#2: Protein/peptide Cyclosporin A


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.) synthetic construct (others) / References: Cyclosporin A
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. HERE, CYCLOSPORIN A IS REPRESENTED BY THE SEQUENCE (SEQRES)
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M citric acid pH 3.5, and 25% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.1→45.09 Å / Num. obs: 154928 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.8
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 7984 / CC1/2: 0.71 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.1→45.09 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.06 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.15301 8309 5.1 %RANDOM
Rwork0.13257 ---
obs0.13359 154928 99.76 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.304 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å2-0 Å21 Å2
2---0.67 Å2-0 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.1→45.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3256 0 0 470 3726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0173446
X-RAY DIFFRACTIONr_bond_other_d0.0010.0193304
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.8644686
X-RAY DIFFRACTIONr_angle_other_deg1.172.6467623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3375436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.29521.591176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.96415554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5891523
X-RAY DIFFRACTIONr_chiral_restr0.1050.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023997
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02809
X-RAY DIFFRACTIONr_mcbond_it1.0731.6261735
X-RAY DIFFRACTIONr_mcbond_other1.0731.6261734
X-RAY DIFFRACTIONr_mcangle_it1.4832.452179
X-RAY DIFFRACTIONr_mcangle_other1.4832.452180
X-RAY DIFFRACTIONr_scbond_it1.31.8451711
X-RAY DIFFRACTIONr_scbond_other1.31.8461712
X-RAY DIFFRACTIONr_scangle_other1.6492.6852498
X-RAY DIFFRACTIONr_long_range_B_refined2.83820.9963835
X-RAY DIFFRACTIONr_long_range_B_other2.31420.193716
X-RAY DIFFRACTIONr_rigid_bond_restr1.77136750
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 640 -
Rwork0.228 11349 -
obs--98.96 %

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