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- PDB-4s1j: Crystal structure of cyclophilin mutant V33A from Leishmania dono... -

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Basic information

Entry
Database: PDB / ID: 4s1j
TitleCrystal structure of cyclophilin mutant V33A from Leishmania donovani at 2.3 angstrom.
ComponentsPeptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / Rotamase / peptidyl-prolyl cis-trans isomerase / Cytosol
Function / homology
Function and homology information


RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / cyclosporin A binding / peptidylprolyl isomerase / 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: 2.3 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 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 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)38,0932
Polymers38,0932
Non-polymers00
Water1,964109
1
A: Peptidyl-prolyl cis-trans isomerase


Theoretical massNumber of molelcules
Total (without water)19,0471
Polymers19,0471
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)19,0471
Polymers19,0471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.534, 48.534, 141.696
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: 19046.553 Da / Num. of mol.: 2 / Fragment: Cyclophilin, peptidyl-prolyl cis-trans-isomerase / Mutation: V33A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Strain: BPK282A1 / Gene: CYP, LDBPK_060120 / Plasmid: pQE32 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: E9B8M3, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% PEG3350, 0.02 M Tris-HCl, 0.02% azide, 7 mg/mL protein, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 23, 2011
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→48.53 Å / Num. all: 14471 / Num. obs: 14068 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 13.8
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.3-2.38181.7
2.38-2.48192.6
2.48-2.59199.9
2.59-2.73199.9
2.73-2.91100
2.9-3.121100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
CNS1.1refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HAQ

2haq


Resolution: 2.3→48.5 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2215 692 -RANDOM
Rwork0.1913 ---
obs0.29 13720 94.4 %-
all-14537 --
Displacement parametersBiso mean: 33.83 Å2
Baniso -1Baniso -2Baniso -3
1-2.184 Å22.184 Å2-4.369 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2568 0 0 109 2677
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5

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