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- PDB-3ni6: Crystal structure of the FK506 binding domain of Plasmodium vivax... -

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Basic information

Entry
Database: PDB / ID: 3ni6
TitleCrystal structure of the FK506 binding domain of Plasmodium vivax FKBP35
Components70 kDa peptidylprolyl isomerase
KeywordsISOMERASE / FK506 binding domain
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity
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 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 profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
peptidylprolyl isomerase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsQureshi, I.A. / Yoon, H.S. / Lescar, J.
CitationJournal: EUKARYOTIC CELL / Year: 2013
Title: Structural insights into substrate binding by PvFKBP35, a peptidylprolyl cis-trans isomerase from the human malarial parasite Plasmodium vivax
Authors: Alag, R. / Balakrishna, A.M. / Rajan, S. / Qureshi, I.A. / Shin, J. / Lescar, J. / Gruber, G. / Yoon, H.S.
History
DepositionJun 15, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 9, 2013Group: Database references
Revision 1.3Nov 1, 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_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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)28,68010
Polymers27,9432
Non-polymers7378
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-6 kcal/mol
Surface area12950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.917, 41.857, 55.339
Angle α, β, γ (deg.)90.00, 106.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 70 kDa peptidylprolyl isomerase


Mass: 13971.687 Da / Num. of mol.: 2 / Fragment: FK506-BINDING DOMAIN, RESIDUES 1-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A5K8X6
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 4000, 0.1M Tris HCl, 0.2M magnesium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 2009 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.42→30 Å / Num. all: 45546 / Num. obs: 44603 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 %
Reflection shellResolution: 1.42→1.47 Å / Redundancy: 4.4 % / % possible all: 88.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IHZ

3ihz


Resolution: 1.42→22.67 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.363 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21872 2249 5.1 %RANDOM
Rwork0.17071 ---
all0.17307 45546 --
obs0.17307 42266 97.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.028 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å2-0.01 Å2
2--0.04 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.42→22.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1897 0 48 278 2223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222028
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.9822720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4635263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.80725.31994
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94915381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9571510
X-RAY DIFFRACTIONr_chiral_restr0.0990.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021500
X-RAY DIFFRACTIONr_mcbond_it1.6111.51227
X-RAY DIFFRACTIONr_mcangle_it2.49721981
X-RAY DIFFRACTIONr_scbond_it3.4123801
X-RAY DIFFRACTIONr_scangle_it5.3174.5729
X-RAY DIFFRACTIONr_rigid_bond_restr1.93932028
X-RAY DIFFRACTIONr_sphericity_free6.1213278
X-RAY DIFFRACTIONr_sphericity_bonded4.58231995
LS refinement shellResolution: 1.422→1.459 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 149 -
Rwork0.269 2695 -
obs--85.46 %

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