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- PDB-4s1e: Crystal structure of cyclophilin mutant L120A from Leishmania don... -

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Basic information

Entry
Database: PDB / ID: 4s1e
TitleCrystal structure of cyclophilin mutant L120A from Leishmania donovani at 2.22 angstrom.
ComponentsPeptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / Cytosol
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
Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsRoy, S. / Datta, A.K. / Banerjee, R.
CitationJournal: To be Published
Title: Characterization and prediction of thermal stability of cyclophilin mutants from L.donovani
Authors: Roy, S. / Datta, A.K. / Banerjee, R.
History
DepositionJan 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)38,0652
Polymers38,0652
Non-polymers00
Water2,144119
1
A: Peptidyl-prolyl cis-trans isomerase


Theoretical massNumber of molelcules
Total (without water)19,0331
Polymers19,0331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase


Theoretical massNumber of molelcules
Total (without water)19,0331
Polymers19,0331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.619, 48.619, 141.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase


Mass: 19032.525 Da / Num. of mol.: 2 / Fragment: residues 22-187 / Mutation: L120A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DEPOSITOR STATES THAT THE PRIMARY SEQUENCE WAS RE-SEQUENCED AND ERRORS WERE DETECTED AT ...THE DEPOSITOR STATES THAT THE PRIMARY SEQUENCE WAS RE-SEQUENCED AND ERRORS WERE DETECTED AT POSITIONS 81 AND 112. THE ACTUAL SEQUENCE WAS FOUND TO BE PRO 81 AND LYS 112, WHICH WAS ALSO CONFIRMED IN THE ELECTRON DENSITY MAP OF THE STRUCTURE.

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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: 43.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% PEG 3350,0.02 M Tris-HCl,0.02% Azide, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Sep 12, 2011
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.22→30 Å / Num. all: 16104 / Num. obs: 16104 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.91 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 23.8
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.22-2.3193.7
2.3-2.391100
2.39-2.51100
2.5-2.631100
2.63-2.791100
2.79-3.011100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HAQ

2haq


Resolution: 2.22→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2216 784 RANDOM
Rwork0.1756 --
obs0.243 16064 -
all-16339 -
Displacement parametersBiso mean: 30.85 Å2
Baniso -1Baniso -2Baniso -3
1-2.464 Å22.464 Å2-4.928 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.22→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2566 0 0 119 2685
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5

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