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- PDB-7uss: Plasmodium falciparum protein Pfs230 Pro-D1D2 - Structure of the ... -

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Basic information

Entry
Database: PDB / ID: 7uss
TitlePlasmodium falciparum protein Pfs230 Pro-D1D2 - Structure of the first two 6-cysteine domains with N-terminal extension
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 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.2Oct 25, 2023Group: 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
B: Gametocyte surface protein P230
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4816
Polymers82,6112
Non-polymers8704
Water6,792377
1
A: Gametocyte surface protein P230
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9153
Polymers41,3061
Non-polymers6102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Gametocyte surface protein P230
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5663
Polymers41,3061
Non-polymers2602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.250, 50.853, 108.965
Angle α, β, γ (deg.)99.190, 98.860, 94.660
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 555 through 596 or resid 598...
21(chain B and (resid 555 through 588 or (resid 589...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 555 through 596 or resid 598...A555 - 596
121(chain A and (resid 555 through 596 or resid 598...A598 - 613
131(chain A and (resid 555 through 596 or resid 598...A614
141(chain A and (resid 555 through 596 or resid 598...A555 - 900
151(chain A and (resid 555 through 596 or resid 598...A555 - 900
161(chain A and (resid 555 through 596 or resid 598...A615
171(chain A and (resid 555 through 596 or resid 598...A555 - 900
211(chain B and (resid 555 through 588 or (resid 589...B555 - 588
221(chain B and (resid 555 through 588 or (resid 589...B589
231(chain B and (resid 555 through 588 or (resid 589...B555 - 898
241(chain B and (resid 555 through 588 or (resid 589...B555 - 898
251(chain B and (resid 555 through 588 or (resid 589...B555 - 898
261(chain B and (resid 555 through 588 or (resid 589...B555 - 898
271(chain B and (resid 555 through 588 or (resid 589...B555 - 898

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Components

#1: Protein Gametocyte surface protein P230


Mass: 41305.680 Da / Num. of mol.: 2
Fragment: first two 6-cysteine domains with N-terminal extension
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / 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: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: K
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 30% PEG MME 2000, 0.1 M potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 1.9→48.54 Å / Num. obs: 56540 / % possible obs: 97.3 % / Redundancy: 3.643 % / Biso Wilson estimate: 35.303 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.102 / Χ2: 0.844 / Net I/σ(I): 9.44 / Num. measured all: 205972
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
1.9-2.013.4950.7381.5731105937789010.6850.87294.9
2.01-2.153.7920.4782.6232478882685640.8410.55697
2.15-2.323.7430.3133.9430105825480440.9140.36597.5
2.32-2.543.6530.2215.3527003758073920.9550.25997.5
2.54-2.843.4860.1387.8623257682566710.980.16397.7
2.84-3.283.7230.08413.6121982601259050.9930.09898.2
3.28-4.013.7140.05122.4518721511650410.9970.05998.5
4.01-5.663.4770.03828.8813444394938670.9970.04597.9
5.66-48.543.6550.03431.637877218621550.9980.0498.6

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7USR

7usr


Resolution: 1.9→48.54 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.95 / Phase error: 22.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2068 2823 5 %
Rwork0.1773 53633 -
obs0.1788 56456 97.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.1 Å2 / Biso mean: 41.1399 Å2 / Biso min: 15.52 Å2
Refinement stepCycle: final / Resolution: 1.9→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4845 0 54 377 5276
Biso mean--75.33 42.05 -
Num. residues----621
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1784X-RAY DIFFRACTION6.531TORSIONAL
12B1784X-RAY DIFFRACTION6.531TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.93280.3081400.2876266396
1.9328-1.96790.31511420.2668269997
1.9679-2.00580.27811370.2559260397
2.0058-2.04670.28551430.2358271597
2.0467-2.09120.26691400.2227264897
2.0912-2.13990.261400.2096266997
2.1399-2.19340.26241420.2091269297
2.1934-2.25270.251380.1963263497
2.2527-2.3190.22341430.1835270798
2.319-2.39390.22721400.1889265697
2.3939-2.47940.2031410.1901269298
2.4794-2.57870.22071420.1811268998
2.5787-2.6960.22461430.1754271998
2.696-2.83810.23981400.1851264898
2.8381-3.01590.2261410.172268898
3.0159-3.24880.20021420.1803269598
3.2488-3.57560.18721440.1701273099
3.5756-4.09280.19851410.1506268198
4.0928-5.15550.14461420.1318270298
5.1555-48.50.17191420.1732270398
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)
11.4764-0.06280.20111.6401-1.20693.09170.00930.0686-0.0177-0.00050.02560.03860.0658-0.0822-0.03810.15680.01470.00950.1603-0.0420.227-13.10894.715557.0791
20.9309-0.31490.25741.8106-2.49235.78970.07660.43080.2258-0.1953-0.2824-0.2596-0.25360.65120.20590.332-0.0290.04890.43150.03640.3181-9.451316.253731.7417
32.0465-0.13961.39732.5814-0.5394.81760.01930.3177-0.0632-0.7230.20170.24980.2501-0.4104-0.15990.3809-0.0595-0.03850.39890.06830.2448-22.710413.881824.8622
40.5957-0.3365-0.72394.954-1.32182.5895-0.03520.0189-0.1191-0.2155-0.024-0.33090.2227-0.10580.04140.2239-0.0102-0.01820.26850.00380.23796.771819.773672.8616
51.00870.00070.5142.6964-2.86717.2720.0598-0.17970.11210.523-0.01550.0028-0.6586-0.0211-0.04080.2969-0.00290.01880.2053-0.05660.2807-0.463731.183283.2825
60.35060.4766-0.44312.3554-1.19973.14750.0633-0.1364-0.0341-0.052-0.00380.07940.102-0.0655-0.06850.1579-0.0127-0.00490.1705-0.01870.212-0.225818.056778.7265
71.78090.0580.66952.2759-2.17475.74490.0604-0.11550.00620.08730.02880.1461-0.0385-0.1209-0.08930.17520.02420.00930.1708-0.04680.2351-2.097122.662679.8377
80.85440.2222-0.50741.8448-2.14035.08510.0274-0.4572-0.07970.3517-0.0772-0.00590.47310.30220.09930.5548-0.0033-0.03520.44710.01220.2983-0.63039.7377107.4915
92.3219-0.1659-0.89191.0129-0.08773.51570.0173-0.35670.02830.5291-0.00880.08680.1835-0.3475-0.02880.52-0.06420.00350.40820.03360.2346-6.349512.5985108.8369
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 555 through 719 )A555 - 719
2X-RAY DIFFRACTION2chain 'A' and (resid 720 through 802 )A720 - 802
3X-RAY DIFFRACTION3chain 'A' and (resid 803 through 887 )A803 - 887
4X-RAY DIFFRACTION4chain 'B' and (resid 555 through 579 )B555 - 579
5X-RAY DIFFRACTION5chain 'B' and (resid 580 through 625 )B580 - 625
6X-RAY DIFFRACTION6chain 'B' and (resid 626 through 676 )B626 - 676
7X-RAY DIFFRACTION7chain 'B' and (resid 677 through 719 )B677 - 719
8X-RAY DIFFRACTION8chain 'B' and (resid 720 through 822 )B720 - 822
9X-RAY DIFFRACTION9chain 'B' and (resid 823 through 887 )B823 - 887

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