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- PDB-4ys4: Crystal structure of Pf41 tandem 6-cys domains from Plasmodium fa... -

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Basic information

Entry
Database: PDB / ID: 4ys4
TitleCrystal structure of Pf41 tandem 6-cys domains from Plasmodium falciparum
ComponentsMerozoite surface protein P41
KeywordsIMMUNE SYSTEM / Antigens
Function / homology
Function and homology information


symbiont-containing vacuolar space / cell surface / plasma membrane
Similarity search - Function
Immunoglobulin-like - #2860 / : / 6-Cysteine (6-Cys) domain / 6-Cysteine (6-Cys) domain superfamily / Sexual stage antigen s48/45 domain / 6-Cysteine (6-Cys) domain profile. / Sexual stage antigen s48/45 domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Merozoite surface protein P41
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsParker, M.L. / Peng, F. / Boulanger, M.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Plos One / Year: 2015
Title: The Structure of Plasmodium falciparum Blood-Stage 6-Cys Protein Pf41 Reveals an Unexpected Intra-Domain Insertion Required for Pf12 Coordination.
Authors: Parker, M.L. / Peng, F. / Boulanger, M.J.
History
DepositionMar 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Merozoite surface protein P41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6837
Polymers41,3241
Non-polymers3596
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.760, 133.760, 133.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-552-

HOH

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Components

#1: Protein Merozoite surface protein P41


Mass: 41323.812 Da / Num. of mol.: 1 / Fragment: 6-Cys 1 and 2 domains, residues 21-378 / Mutation: S49A, S71A, S79A, S151A, T184A, S207A, S353A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: PF41, PFD0240c / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8I1Y0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 3.41 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.01 M zinc chloride, 0.1 M MES buffer pH 6.0, 20% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 26, 2014
RadiationMonochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.45→47.29 Å / Num. all: 14643 / Num. obs: 14643 / % possible obs: 99 % / Redundancy: 10.2 % / Biso Wilson estimate: 44.7 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 18.2
Reflection shellResolution: 2.45→2.57 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 3 / % possible all: 92.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
Cootmodel building
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.45→42.299 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 696 4.76 %random selection
Rwork0.1823 13941 --
obs0.1844 14637 98.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.05 Å2 / Biso mean: 48.8639 Å2 / Biso min: 25.63 Å2
Refinement stepCycle: final / Resolution: 2.45→42.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2087 0 11 54 2152
Biso mean--65.24 45.76 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032142
X-RAY DIFFRACTIONf_angle_d0.7462881
X-RAY DIFFRACTIONf_chiral_restr0.031313
X-RAY DIFFRACTIONf_plane_restr0.003372
X-RAY DIFFRACTIONf_dihedral_angle_d13.703798
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.63950.30411420.24792638278095
2.6395-2.9050.30961250.237827952920100
2.905-3.32520.28251420.216127952937100
3.3252-4.18890.21711390.172428192958100
4.1889-42.30490.18121480.149628943042100

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