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- PDB-8e1z: Crystal structure of Plasmodium falciparum ookinete surface antig... -

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Basic information

Entry
Database: PDB / ID: 8e1z
TitleCrystal structure of Plasmodium falciparum ookinete surface antigen Pfs28
ComponentsOokinete surface protein Pfs28
KeywordsCELL ADHESION / Transmission blocking vaccine
Function / homologyOokinete surface antigen, EGF domain / Pvs28 EGF domain / Epidermal growth factor-like domain. / EGF-like domain / cell surface / membrane / Ookinete surface protein Pfs28
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShukla, N. / Tang, W.K. / Tolia, N.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1ZIAAI001237 United States
CitationJournal: Sci Rep / Year: 2022
Title: Structural analysis of Plasmodium falciparum ookinete surface antigen Pfs28 relevant for malaria vaccine design.
Authors: Shukla, N. / Tang, W.K. / Tolia, N.H.
History
DepositionAug 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ookinete surface protein Pfs28
B: Ookinete surface protein Pfs28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8034
Polymers40,6722
Non-polymers1322
Water57632
1
A: Ookinete surface protein Pfs28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4322
Polymers20,3361
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ookinete surface protein Pfs28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3712
Polymers20,3361
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.730, 74.180, 69.820
Angle α, β, γ (deg.)90.000, 105.170, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Ookinete surface protein Pfs28


Mass: 20335.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Plasmid: pHL-Sec / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q6LEB4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.2 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.5M ammonium sulfate and 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→34.59 Å / Num. obs: 15434 / % possible obs: 97.73 % / Redundancy: 3.4 % / Biso Wilson estimate: 40.47 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.1181 / Rpim(I) all: 0.07575 / Rrim(I) all: 0.1408 / Net I/σ(I): 7.02
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 1579 / CC1/2: 0.772 / CC star: 0.933 / Rpim(I) all: 0.4288 / Rrim(I) all: 0.8032 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AF-Q8IJ96-F1

Resolution: 2.3→34.59 Å / SU ML: 0.3195 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 31.5329
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2773 1528 9.93 %
Rwork0.2346 13865 -
obs0.2389 15393 97.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.91 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2406 0 6 32 2444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00292441
X-RAY DIFFRACTIONf_angle_d0.56663294
X-RAY DIFFRACTIONf_chiral_restr0.0433375
X-RAY DIFFRACTIONf_plane_restr0.0026427
X-RAY DIFFRACTIONf_dihedral_angle_d9.2753912
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.34631440.30071283X-RAY DIFFRACTION98.69
2.37-2.460.34161330.28931242X-RAY DIFFRACTION97.73
2.46-2.560.32581360.28181256X-RAY DIFFRACTION96.94
2.56-2.670.41581380.29531249X-RAY DIFFRACTION97.54
2.67-2.810.31851390.2821247X-RAY DIFFRACTION98.23
2.82-2.990.31931340.27541284X-RAY DIFFRACTION98.27
2.99-3.220.32181380.28161247X-RAY DIFFRACTION97.81
3.22-3.550.29791380.22851262X-RAY DIFFRACTION97.83
3.55-4.060.2341400.1941231X-RAY DIFFRACTION95.74
4.06-5.110.19841430.17881279X-RAY DIFFRACTION98.68
5.11-100.27081450.23441285X-RAY DIFFRACTION97.81

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