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- PDB-2vn1: Crystal structure of the FK506-binding domain of Plasmodium falci... -

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Basic information

Entry
Database: PDB / ID: 2vn1
TitleCrystal structure of the FK506-binding domain of Plasmodium falciparum FKBP35 in complex with FK506
Components70 KDA PEPTIDYLPROLYL ISOMERASE
KeywordsISOMERASE / FKBP / FK506 / TPR REPEAT / PLASMODIUM FALCIPARUM
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
8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / Peptidyl-prolyl cis-trans isomerase FKBP35
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsKotaka, M. / Alag, R. / Ye, H. / Preiser, P.R. / Yoon, H.S. / Lescar, J.
CitationJournal: Biochemistry / Year: 2008
Title: Crystal Structure of the Fk506 Binding Domain of Plasmodium Falciparum Fkbp35 in Complex with Fk506.
Authors: Kotaka, M. / Ye, H. / Alag, R. / Hu, G. / Bozdech, Z. / Preiser, P.R. / Yoon, H.S. / Lescar, J.
History
DepositionJan 30, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 70 KDA PEPTIDYLPROLYL ISOMERASE
B: 70 KDA PEPTIDYLPROLYL ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6714
Polymers29,0632
Non-polymers1,6082
Water2,918162
1
A: 70 KDA PEPTIDYLPROLYL ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3352
Polymers14,5311
Non-polymers8041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 70 KDA PEPTIDYLPROLYL ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3352
Polymers14,5311
Non-polymers8041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)63.064, 63.064, 167.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.7224, -0.6915, 0.0035), (0.6914, -0.7223, -0.0146), (0.0126, -0.0081, 0.9999)
Vector: 22.2011, 54.699, 21.2802)

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Components

#1: Protein 70 KDA PEPTIDYLPROLYL ISOMERASE / PLASMODIUM FALCIPARUM FKBP35


Mass: 14531.420 Da / Num. of mol.: 2 / Fragment: FK506-BINDING DOMAIN, RESIDUES 1-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Strain: 3D7 / Plasmid: PET29B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8I4V8, peptidylprolyl isomerase
#2: Chemical ChemComp-FK5 / 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / K506 / Tacrolimus


Mass: 804.018 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H69NO12 / Comment: medication*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.97 Å3/Da / Density % sol: 58.6 % / Description: NONE
Crystal growpH: 5 / Details: 2.7M NA MALONATE, PH5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 24, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 14883 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 20.7 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 41.1
Reflection shellResolution: 2.35→2.43 Å / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 8.5 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YAT

1yat


Resolution: 2.35→29.65 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1800752.84 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.25 733 4.9 %RANDOM
Rwork0.194 ---
obs0.194 14825 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.8564 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 35.5 Å2
Baniso -1Baniso -2Baniso -3
1-6.66 Å20 Å20 Å2
2--6.66 Å20 Å2
3----13.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.35→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 114 162 2214
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.074
X-RAY DIFFRACTIONc_mcangle_it6.528
X-RAY DIFFRACTIONc_scbond_it10.058
X-RAY DIFFRACTIONc_scangle_it11.9112
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.348 113 4.7 %
Rwork0.275 2269 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2FK5_PRODRG.PARFK5_PRODRG.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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