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- PDB-6l2b: Crystal structure of cyclophilin mutant I164M from Leishmania don... -

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Basic information

Entry
Database: PDB / ID: 6l2b
TitleCrystal structure of cyclophilin mutant I164M from Leishmania donovani at 2.65 angstrom resolution
ComponentsPeptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / Peptidyl prolyl isomerase / 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
Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsGhosh, S. / Biswas, G. / Datta, A.K. / Banerjee, R.
Citation
Journal: To Be Published
Title: Crystal structure of cyclophilin mutant I164M from Leishmania donovani at 2.65 angstrom resolution.
Authors: Ghosh, S. / Biswas, G. / Datta, A.K. / Banerjee, R.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2007
Title: Structure of cyclophilin from Leishmania donovani at 1.97 A resolution.
Authors: Venugopal, V. / Sen, B. / Datta, A.K. / Banerjee, R.
History
DepositionOct 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase


Theoretical massNumber of molelcules
Total (without water)19,1091
Polymers19,1091
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7630 Å2
Unit cell
Length a, b, c (Å)48.618, 48.618, 141.322
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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


Mass: 19108.578 Da / Num. of mol.: 1 / Mutation: I164M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Gene: CYP / Plasmid: pQE32 / Production host: Escherichia coli M15 (bacteria) / References: UniProt: Q9U9R3, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.9 % / Description: Tetragonal bipyramid
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20mM Tris HCl, 100mM NaCl, 0.02% sodium azide, PEG 3350 (Reservoir 30% and precipitant 3% in the final drop), protein at concentration 5 mg/ml.

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5406 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 30, 2019
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.65→45.97 Å / Num. obs: 5381 / % possible obs: 99.83 % / Redundancy: 5.58 % / Biso Wilson estimate: 44.16 Å2 / Rmerge(I) obs: 0.102 / Rrim(I) all: 0.112 / Χ2: 1.15 / Net I/σ(I): 10.3
Reflection shellResolution: 2.651→2.746 Å / Redundancy: 5.58 % / Rmerge(I) obs: 0.102 / Num. unique obs: 5384 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
CrystalClear2data reduction
CrystalClear2data scaling
CrystalClear2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HAQ

2haq


Resolution: 2.65→45.97 Å / SU ML: 0.3601 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.4865
RfactorNum. reflection% reflectionSelection details
Rfree0.223 269 5 %Random selection
Rwork0.1775 ---
obs-5381 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.65 Å2
Refinement stepCycle: LAST / Resolution: 2.65→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1274 0 0 41 1315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00231304
X-RAY DIFFRACTIONf_angle_d0.51031763
X-RAY DIFFRACTIONf_chiral_restr0.0472192
X-RAY DIFFRACTIONf_plane_restr0.0033232
X-RAY DIFFRACTIONf_dihedral_angle_d2.6326761
LS refinement shellResolution: 2.651→2.7457 Å
RfactorNum. reflection% reflection
Rfree0.3029 129 -
Rwork0.2124 2467 -
obs--99.92 %

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