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- PDB-9ls5: Entamoeba histolytica Cyclophilin 18 (apo) -

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Basic information

Entry
Database: PDB / ID: 9ls5
TitleEntamoeba histolytica Cyclophilin 18 (apo)
ComponentsPeptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / cyclophilin / PPIase
Function / homology
Function and homology information


cyclosporin A binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesEntamoeba histolytica HM-1:IMSS (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGandhi, S. / Vasudevan, D.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: To Be Published
Title: Crystal structure of Entamoeba histolytica cyclophilin 18
Authors: Gandhi, S. / Vasudevan, D.
History
DepositionFeb 3, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5884
Polymers38,4682
Non-polymers1202
Water3,711206
1
A: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2942
Polymers19,2341
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2942
Polymers19,2341
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.401, 74.077, 62.813
Angle α, β, γ (deg.)90.00, 104.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 19234.076 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica HM-1:IMSS (eukaryote)
Gene: EHI_125840 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LEMO21 / References: UniProt: A0A8U0WPD6, peptidylprolyl isomerase
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.19 Å3/Da / Density % sol: 43.93 % / Description: Rod Shaped
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 20% v/v 2-Propanol, 20% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.4→35.26 Å / Num. obs: 62683 / % possible obs: 96.16 % / Redundancy: 2.2 % / CC1/2: 0.996 / Net I/σ(I): 9.6
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2 / Num. unique obs: 3084 / CC1/2: 0.752 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→35.26 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1895 3162 5.05 %
Rwork0.1588 --
obs0.1604 62653 96.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→35.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2538 0 8 206 2752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052604
X-RAY DIFFRACTIONf_angle_d0.8943509
X-RAY DIFFRACTIONf_dihedral_angle_d6.317352
X-RAY DIFFRACTIONf_chiral_restr0.09377
X-RAY DIFFRACTIONf_plane_restr0.005461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.23881070.20222580X-RAY DIFFRACTION96
1.42-1.440.22061210.18562623X-RAY DIFFRACTION95
1.44-1.470.25851100.18072547X-RAY DIFFRACTION96
1.47-1.490.21861270.17062563X-RAY DIFFRACTION95
1.49-1.520.22771340.15152560X-RAY DIFFRACTION95
1.52-1.550.19411470.14992498X-RAY DIFFRACTION93
1.55-1.580.20041560.14032558X-RAY DIFFRACTION96
1.58-1.610.17721400.13652559X-RAY DIFFRACTION95
1.61-1.650.20171240.14162579X-RAY DIFFRACTION96
1.65-1.690.20441520.14632592X-RAY DIFFRACTION97
1.69-1.740.18071430.1352583X-RAY DIFFRACTION97
1.74-1.790.17711480.13412613X-RAY DIFFRACTION97
1.79-1.850.16091480.1312593X-RAY DIFFRACTION96
1.85-1.910.19281370.14212495X-RAY DIFFRACTION94
1.91-1.990.18741190.14522615X-RAY DIFFRACTION97
1.99-2.080.17811400.15012602X-RAY DIFFRACTION96
2.08-2.190.1571390.14832649X-RAY DIFFRACTION98
2.19-2.330.20671520.15542628X-RAY DIFFRACTION98
2.33-2.510.17381410.16592603X-RAY DIFFRACTION97
2.51-2.760.20061370.17592585X-RAY DIFFRACTION96
2.76-3.160.22431650.18812612X-RAY DIFFRACTION97
3.16-3.980.20771280.1712638X-RAY DIFFRACTION97
3.98-35.260.14741470.14972616X-RAY DIFFRACTION95

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