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- PDB-7usr: Plasmodium falciparum protein Pfs230 D1D2 - Structure of the firs... -

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Basic information

Entry
Database: PDB / ID: 7usr
TitlePlasmodium falciparum protein Pfs230 D1D2 - Structure of the first two 6-cysteine domains
ComponentsGametocyte surface protein P230
KeywordsCELL ADHESION / 6-cysteine protein / s48/45 domain / Plasmodium
Function / homology6-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 / cell surface / plasma membrane / Gametocyte surface protein P230
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsDietrich, M.H. / Tham, W.H.
Funding support Australia, United Kingdom, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP2001385 Australia
Wellcome Trust208693/Z/17/Z United Kingdom
CitationJournal: Biochem.J. / Year: 2022
Title: Nanobodies against Pfs230 block Plasmodium falciparum transmission.
Authors: Dietrich, M.H. / Gabriela, M. / Reaksudsan, K. / Dixon, M.W.A. / Chan, L.J. / Adair, A. / Trickey, S. / O'Neill, M.T. / Tan, L.L. / Lopaticki, S. / Healer, J. / Keremane, S. / Cowman, A.F. / Tham, W.H.
History
DepositionApr 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gametocyte surface protein P230
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9812
Polymers35,4101
Non-polymers5711
Water5,368298
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.788, 65.788, 108.035
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Gametocyte surface protein P230


Mass: 35410.430 Da / Num. of mol.: 1 / Fragment: first two 6-cysteine domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: PFS230, PF230, S230, PF3D7_0209000 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P68874
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.3 Å3/Da / Density % sol: 62.74 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.968625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968625 Å / Relative weight: 1
ReflectionResolution: 1.93→46.519 Å / Num. obs: 34715 / % possible obs: 99.9 % / Redundancy: 14.187 % / Biso Wilson estimate: 34.761 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.139 / Rrim(I) all: 0.144 / Χ2: 1.054 / Net I/σ(I): 16.64 / Num. measured all: 492491
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.93-2.0414.2051.441.9379050559555650.7321.49499.5
2.04-2.1814.4890.8513.4575995524552450.8850.882100
2.18-2.3614.2530.5715.1469895490449040.9540.592100
2.36-2.5813.4370.3857.2960774452345230.9730.4100
2.58-2.8914.0830.22112.457458408040800.9910.229100
2.89-3.3314.7780.11823.1553438361636160.9980.122100
3.33-4.0714.4320.05943.0244278306830680.9990.061100
4.07-5.7413.1810.04257.2231095235923590.9990.044100
5.74-46.51915.1350.03766205081357135510.03999.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.15_3459refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished, in-house structure of a Pt-derivative solved by SIRAS

Resolution: 1.93→46.519 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2051 2071 6 %
Rwork0.1635 32445 -
obs0.166 34516 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.04 Å2 / Biso mean: 40.2139 Å2 / Biso min: 17.31 Å2
Refinement stepCycle: final / Resolution: 1.93→46.519 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2264 0 38 298 2600
Biso mean--108.53 45.61 -
Num. residues----288
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.93-1.97490.30261390.25152176
1.9749-2.02430.27141370.22842138
2.0243-2.07910.25131360.20252141
2.0791-2.14020.24241380.19742159
2.1402-2.20930.22411390.18292175
2.2093-2.28830.22741370.17572146
2.2883-2.37990.18821380.16942155
2.3799-2.48820.22721370.16492152
2.4882-2.61940.2061380.16722156
2.6194-2.78350.19671380.16532164
2.7835-2.99840.21421390.1682188
2.9984-3.30.22831380.16812153
3.3-3.77740.18691380.15522170
3.7774-4.75830.18351390.12682171
4.7583-46.5190.17571400.15882201
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)
12.03011.4135-1.79052.4752-2.35354.5456-0.0546-0.0492-0.0306-0.1015-0.0168-0.04760.14120.04270.07050.15160.02050.00180.1386-0.01320.16669.496240.8302-26.3598
22.98041.8093-0.63714.97190.61466.8044-0.17330.36170.2629-0.20370.24430.60080.159-0.6947-0.07210.2321-0.0312-0.01540.27610.0850.248154.118223.0593-4.6482
31.5587-0.32980.15411.5411-0.81823.2554-0.05670.0253-0.2437-0.0872-0.2532-0.46490.53340.54090.26560.27010.04180.05330.24850.03870.332969.227120.8066-1.9
45.55220.9565-0.09131.5912-0.92956.7666-0.017-0.12940.17850.0255-0.1329-0.2099-0.2682-0.34620.20590.21540.0038-0.01110.16160.04850.166159.691722.37726.7032
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 587 through 734 )A587 - 734
2X-RAY DIFFRACTION2chain 'A' and (resid 735 through 802 )A735 - 802
3X-RAY DIFFRACTION3chain 'A' and (resid 803 through 857 )A803 - 857
4X-RAY DIFFRACTION4chain 'A' and (resid 858 through 887 )A858 - 887

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