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- PDB-4jys: Crystal structure of FKBP25 from Plasmodium Vivax -

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Basic information

Entry
Database: PDB / ID: 4jys
TitleCrystal structure of FKBP25 from Plasmodium Vivax
ComponentsPeptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / Plasmodium Vivax / Non-Canonical / FKBP / FKBP25
Function / homology
Function and homology information


RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase
Similarity search - Function
Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / peptidylprolyl isomerase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSreekanth, R. / Yoon, H.S.
CitationJournal: Proteins / Year: 2014
Title: Crystal structure of Plasmodium vivax FK506-binding protein 25 reveals conformational changes responsible for its noncanonical activity
Authors: Rajan, S. / Austin, D. / Harikishore, A. / Nguyen, Q.T. / Baek, K. / Yoon, H.S.
History
DepositionApr 1, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)32,3517
Polymers32,1072
Non-polymers2455
Water4,017223
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Peptidyl-prolyl cis-trans isomerase
hetero molecules

B: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3517
Polymers32,1072
Non-polymers2455
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
Buried area1400 Å2
ΔGint-10 kcal/mol
Surface area13810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.600, 61.910, 99.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase / FK506 binding domain/Calmodulin Binding Domain


Mass: 16053.455 Da / Num. of mol.: 2 / Fragment: UNP residues 72-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Strain: Salvador I / Gene: PVX_122487 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5JZC2
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.5M NaCl, 0.1M Imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 3, 2012 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→35 Å / Num. obs: 23413 / % possible obs: 99.5 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3263 / % possible all: 96.6

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Processing

Software
NameVersionClassification
BALBESphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.148 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: FOR THE STARTING MODEL, THERE IS NO SPECIFIC MODEL AS THIS IS FROM A BALBES SOLUTION
RfactorNum. reflection% reflectionSelection details
Rfree0.22269 1203 5.1 %RANDOM
Rwork0.17509 ---
obs0.17761 22159 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.968 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2004 0 13 223 2240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192065
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.972792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8265244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76724.14994
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05415373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2121510
X-RAY DIFFRACTIONr_chiral_restr0.1310.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211553
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 88 -
Rwork0.26 1496 -
obs--93.07 %

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