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- PDB-2fbn: Plasmodium falciparum putative FK506-binding protein PFL2275c, C-... -

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Basic information

Entry
Database: PDB / ID: 2fbn
TitlePlasmodium falciparum putative FK506-binding protein PFL2275c, C-terminal TPR-containing domain
Components70 kDa peptidylprolyl isomerase, putative
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Sulfur SAD / PFL2275c / TPR-containing domain / Structural Genomics Consortium / SGC
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
Tetratricopeptide repeat domain / Tetratricopeptide repeat / 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 repeat domain / Tetratricopeptide repeat / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
: / Peptidyl-prolyl cis-trans isomerase FKBP35
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.63 Å
AuthorsDong, A. / Lew, J. / Koeieradzki, I. / Sundararajan, E. / Melone, M. / Wasney, G. / Zhao, Y. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. ...Dong, A. / Lew, J. / Koeieradzki, I. / Sundararajan, E. / Melone, M. / Wasney, G. / Zhao, Y. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R. / Hills, T. / Structural Genomics Consortium (SGC)
CitationJournal: Protein Sci. / Year: 2009
Title: Crystallographic structure of the tetratricopeptide repeat domain of Plasmodium falciparum FKBP35 and its molecular interaction with Hsp90 C-terminal pentapeptide.
Authors: Alag, R. / Bharatham, N. / Dong, A. / Hills, T. / Harikishore, A. / Widjaja, A.A. / Shochat, S.G. / Hui, R. / Yoon, H.S.
History
DepositionDec 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: 70 kDa peptidylprolyl isomerase, putative
B: 70 kDa peptidylprolyl isomerase, putative


Theoretical massNumber of molelcules
Total (without water)46,0762
Polymers46,0762
Non-polymers00
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-15 kcal/mol
Surface area16870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.239, 62.936, 103.334
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 70 kDa peptidylprolyl isomerase, putative


Mass: 23037.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Plasmid: P28-LIC-THROMBIN DERIVED FROM SOURCE 9 PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon plus Ril / References: GenBank: 23509147, UniProt: Q8I4V8*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 38.01 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 4.6
Details: 3.5 M NaFormate, 0.1 M NaAcetate pH 4.6, VAPOR DIFFUSION, temperature 296K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceTypeIDWavelengthWavelength (Å)
ROTATING ANODERIGAKU FR-E11.5418
ROTATING ANODERIGAKU RU20022.29
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV1IMAGE PLATEDec 5, 2005VariMax HR
RIGAKU RAXIS IV2IMAGE PLATEDec 7, 2005VeriMax Cr
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1VeriMax HRSINGLE WAVELENGTHMx-ray1
2VeriMax CrSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
22.291
ReflectionResolution: 1.63→50 Å / Num. all: 41003 / Num. obs: 41003 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 19.4
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 1.64 / Num. unique all: 720 / Rsym value: 0.507 / % possible all: 31

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalClear(MSC/RIGAKU)data reduction
HKL-2000data scaling
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CootV. 0.0.33model building
RefinementMethod to determine structure: SAD / Resolution: 1.63→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.798 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.109 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23522 1058 2.6 %RANDOM
Rwork0.19985 ---
all0.2008 41003 --
obs0.2008 39882 87.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 1.63→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2510 0 0 354 2864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222553
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1141.9633427
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5045304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6126.567134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81915509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.331154
X-RAY DIFFRACTIONr_chiral_restr0.0770.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021906
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.21315
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21788
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2248
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.120.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8611.51561
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.43822446
X-RAY DIFFRACTIONr_scbond_it2.49631117
X-RAY DIFFRACTIONr_scangle_it3.8754.5981
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.514 33 -
Rwork0.442 1117 -
obs--34.03 %

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