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- PDB-3pa7: Crystal structure of FKBP from plasmodium vivax in complex with t... -

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Basic information

Entry
Database: PDB / ID: 3pa7
TitleCrystal structure of FKBP from plasmodium vivax in complex with tetrapeptide ALPF
Components
  • 4-mer Peptide ALPF
  • 70 kDa peptidylprolyl isomerase, putative
KeywordsISOMERASE / Plasmodium vivax / FKBP35 / PPIase / FK506 binding protein
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 / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / 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 / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / 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 / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsBalakrishna, A.M. / Alag, R. / Yoon, H.S.
Citation
Journal: 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.
#1: Journal: Protein Sci. / Year: 2010
Title: NMR and crystallographic structures of the FK506 binding domain of human malarial parasite Plasmodium vivax FKBP35
Authors: Alag, R. / Qureshi, I.A. / Bharatham, N. / Shin, J. / Lescar, J. / Yoon, H.S.
History
DepositionOct 18, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
D: 4-mer Peptide ALPF


Theoretical massNumber of molelcules
Total (without water)28,3903
Polymers28,3903
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.963, 41.378, 61.303
Angle α, β, γ (deg.)90.00, 95.02, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 1 / Auth seq-ID: 5 - 125 / Label seq-ID: 5 - 125

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein 70 kDa peptidylprolyl isomerase, putative


Mass: 13971.687 Da / Num. of mol.: 2 / Fragment: residues 1-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Strain: SALVADOR I / Gene: PVX_101260 / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5K8X6, peptidylprolyl isomerase
#2: Protein/peptide 4-mer Peptide ALPF


Mass: 446.539 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 1.98 Å3/Da / Density % sol: 37.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 100mM BICINE, 2.4M Ammonium sulfate, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 30, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.61→30 Å / Num. obs: 6670 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Biso Wilson estimate: 49.2 Å2 / Rmerge(I) obs: 0.028 / Net I/σ(I): 22.03
Reflection shellResolution: 2.61→2.74 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.028 / Mean I/σ(I) obs: 22.03 / Num. unique all: 6660 / % possible all: 89.9

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Processing

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

3ihz


Resolution: 2.61→24.12 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.879 / Occupancy max: 1 / Occupancy min: 1 / SU B: 35.665 / SU ML: 0.345 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.483 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.287 625 9.8 %RANDOM
Rwork0.2366 5737 --
obs0.2417 6362 91.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 99.51 Å2 / Biso mean: 41.4839 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--2.27 Å20 Å21.48 Å2
2--2.83 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.61→24.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1947 0 0 150 2097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221978
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.972653
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9935248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98425.10992
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.44515367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0641510
X-RAY DIFFRACTIONr_chiral_restr0.0840.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211491
X-RAY DIFFRACTIONr_mcbond_it0.5391.51230
X-RAY DIFFRACTIONr_mcangle_it1.01621973
X-RAY DIFFRACTIONr_scbond_it1.093748
X-RAY DIFFRACTIONr_scangle_it1.9654.5680
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 934 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL0.130.05
TIGHT THERMAL0.480.5
LS refinement shellResolution: 2.607→2.674 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.512 40 -
Rwork0.329 375 -
all-415 -
obs--85.22 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1406-0.2585-0.02811.2503-0.11940.4849-0.006-0.043-0.01210.06030.0096-0.0072-0.0017-0.0135-0.00360.0383-0.0119-0.01880.02140.00480.0466-9.4028.6572-25.0155
21.3564-0.0072-0.97061.574-0.40811.3032-0.0571-0.1956-0.0988-0.05080.02070.01-0.05150.33320.03640.0328-0.02280.00760.12480.00010.0094-33.402311.3287-6.0821
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 126
2X-RAY DIFFRACTION2B4 - 126

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