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- SASDH92: Plasmodium falciparum lipocalin: Dimer-tetramer equilibrium throu... -

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Basic information

Entry
Database: SASBDB / ID: SASDH92
SamplePlasmodium falciparum lipocalin: Dimer-tetramer equilibrium through a concentration series (combined batch and SEC-SAXS measurements)
  • Plasmodium falciparum Lipocalin (protein), PfLipocalin, Plasmodium falciparum (isolate 3D7)
Function / homologyCalycin / Parasitophorous vacuolar protein 5, putative
Function and homology information
Biological speciesPlasmodium falciparum (isolate 3D7) (eukaryote)
Contact author
  • Cy M Jeffries (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

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Structure visualization

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Models

Model #3920
Type: atomic / Symmetry: P222
Comment: Tetramer model: volume fractions @ 10, 5, 2, & 1 mg/ml: 0.78, 0.66, 0.44, 0.24 (0.15 from SEC)
Chi-square value: 1.27 / P-value: 0.005535
Model #3921
Type: atomic / Symmetry: P2
Comment: Dimer model: volume fractions @ 10, 5, 2, & 1 mg/ml: 0.22, 0.34, 0.56, 0.76 (0.85 from SEC)
Chi-square value: 1.27 / P-value: 0.005535

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Sample

SampleName: Plasmodium falciparum lipocalin: Dimer-tetramer equilibrium through a concentration series (combined batch and SEC-SAXS measurements)
Specimen concentration: 10 mg/ml
BufferName: 20 mM Tris pH7.5, 150 mM NaCl, 5% v/v glycerol / pH: 7.5
Entity #1964Name: PfLipocalin / Type: protein / Description: Plasmodium falciparum Lipocalin / Formula weight: 22.223 / Num. of mol.: 4 / Source: Plasmodium falciparum (isolate 3D7) / References: UniProt: Q8I2Q0
Sequence: PGNDNNNVNN DGVVHVLSKN IDVKNLQGTF YEIATNASDK IFPGLACRCT KYEFSGLKRD GNLGYVLINF SCARNFIFGE KKSEMTFKLI LNKPLDENTT TVEEFNASIY LVQGNQQILL NGNINIIYAE LNEQNEFEHL ILGGQKSIEP MIIMSKYRTV LLDTYNKLIN ...Sequence:
PGNDNNNVNN DGVVHVLSKN IDVKNLQGTF YEIATNASDK IFPGLACRCT KYEFSGLKRD GNLGYVLINF SCARNFIFGE KKSEMTFKLI LNKPLDENTT TVEEFNASIY LVQGNQQILL NGNINIIYAE LNEQNEFEHL ILGGQKSIEP MIIMSKYRTV LLDTYNKLIN SLYLAGYEPS LLTWPFIIQT DQTFCD

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Experimental information

BeamInstrument name: PETRA III EMBL P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotron / Wavelength: 0.124 Å / Dist. spec. to detc.: 3 mm
DetectorName: Pilatus 6M
Scan
Title: Plasmodium falciparum lipocalin: Dimer-tetramer equilibrium through a concentration series (combined batch and SEC-SAXS measurements)
Measurement date: Apr 8, 2019 / Storage temperature: 20 °C / Cell temperature: 10 °C / Exposure time: 0.05 sec. / Number of frames: 20 / Unit: 1/nm /
MinMax
Q0.0785 4.3106
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 1389 /
MinMax
Q0.247128 4.08388
P(R) point1 1389
R0 10.3
Result
Type of curve: single_conc
Comments: The models displayed in this entry fit the concentration series and SEC-SAXS data as a concentration-dependent tetramer-dimer equilibrium. The volume fraction of the tetramer decreases ...Comments: The models displayed in this entry fit the concentration series and SEC-SAXS data as a concentration-dependent tetramer-dimer equilibrium. The volume fraction of the tetramer decreases systematically as the sample concentration ins decreased, or via dilution through the SEC column (evaluated using SASREFmx in P222 (tetramer) P2 (dimer) symmery). The volume fractions of tetramer are: 10 mg/ml, 0.78; 5 mg/ml, 0.66; 2 mg/ml, 0.44; 1 mg/ml, 0.24 and for SEC, 0.15. Additional SASREFmx models, and their associated volume fractions (that do not differ significantly to the models and volume fractions reported here) are included in the full-entry zip archive.
ExperimentalPorod
MW83 kDa79 kDa
Volume-126 nm3

P(R)GuinierGuinier error
Forward scattering, I00.04827 0.04725 -
Radius of gyration, Rg3.254 nm3.16 nm0.01

MinMax
D-10.3
Guinier point1 121

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