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- PDB-4qt3: Crystal structure resolution of Plasmodium falciparum FK506 bindi... -

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Basic information

Entry
Database: PDB / ID: 4qt3
TitleCrystal structure resolution of Plasmodium falciparum FK506 binding domain (FKBP35) in complex with Rapamycin at 1.4A resolution
ComponentsFK506-binding protein (FKBP)-type peptidyl-propyl isomerase
KeywordsISOMERASE / PPiase / enzyme / rapamycin / FKBP35
Function / homology
Function and homology information


HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / negative regulation of phosphoprotein phosphatase activity / FK506 binding / protein peptidyl-prolyl isomerization / chaperone-mediated protein folding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / protein dimerization activity / nucleus / cytoplasm
Similarity search - Function
Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat ...Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / RAPAMYCIN IMMUNOSUPPRESSANT DRUG / Peptidyl-prolyl cis-trans isomerase FKBP35
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBianchin, A. / Allemand, F. / Bell, A. / Chubb, A.J. / Guichou, J.-F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Two crystal structures of the FK506-binding domain of Plasmodium falciparum FKBP35 in complex with rapamycin at high resolution
Authors: Bianchin, A. / Allemand, F. / Bell, A. / Chubb, A.J. / Guichou, J.-F.
History
DepositionJul 7, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: FK506-binding protein (FKBP)-type peptidyl-propyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2833
Polymers15,2151
Non-polymers1,0682
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.476, 50.157, 57.813
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FK506-binding protein (FKBP)-type peptidyl-propyl isomerase


Mass: 15215.076 Da / Num. of mol.: 1 / Fragment: UNP residues 5-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: FKBP35, PFL2275c / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I4V8, peptidylprolyl isomerase
#2: Chemical ChemComp-DTV / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical ChemComp-RAP / RAPAMYCIN IMMUNOSUPPRESSANT DRUG / Sirolimus


Mass: 914.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H79NO13 / Comment: immunosuppressant, antibiotic*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.36 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M MMT, 25% PEG1500, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2014
RadiationMonochromator: yale mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.4→50.15 Å / Num. all: 28931 / Num. obs: 28857 / % possible obs: 99.5 % / Observed criterion σ(F): 1.8 / Observed criterion σ(I): 12

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0032refinement
PDB_EXTRACT3.14data extraction
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VN1

2vn1


Resolution: 1.4→37.89 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.874 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1871 1466 5.1 %RANDOM
Rwork0.1475 ---
obs0.1494 28809 99.33 %-
all-28857 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.91 Å2 / Biso mean: 22.098 Å2 / Biso min: 12.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.65 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.4→37.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms986 0 73 152 1211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.021158
X-RAY DIFFRACTIONr_bond_other_d0.0070.021137
X-RAY DIFFRACTIONr_angle_refined_deg1.3422.0511569
X-RAY DIFFRACTIONr_angle_other_deg2.3963.0042663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2655146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41725.6653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26715219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.24155
X-RAY DIFFRACTIONr_chiral_restr0.0760.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021269
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02240
X-RAY DIFFRACTIONr_mcbond_it1.5151.942525
X-RAY DIFFRACTIONr_mcbond_other1.4961.936524
X-RAY DIFFRACTIONr_mcangle_it1.9352.911655
X-RAY DIFFRACTIONr_rigid_bond_restr4.50132295
X-RAY DIFFRACTIONr_sphericity_free24.359545
X-RAY DIFFRACTIONr_sphericity_bonded5.83552370
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 127 -
Rwork0.216 1965 -
all-2092 -
obs--98.91 %

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