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- PDB-7kj7: Plasmodium falciparum protein Pf12p -

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Basic information

Entry
Database: PDB / ID: 7kj7
TitlePlasmodium falciparum protein Pf12p
ComponentsSurface protein P12p
KeywordsUNKNOWN FUNCTION / Plasmodium falciparum / 6-cysteine protein / s48/45 domain
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 / Surface protein P12p
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDietrich, M.H. / Tham, W.H.
Funding support Australia, United Kingdom, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1154937 Australia
Wellcome Trust208693/Z/17/Z United Kingdom
CitationJournal: Biochem.J. / Year: 2021
Title: Nanobody generation and structural characterization of Plasmodium falciparum 6-cysteine protein Pf12p.
Authors: Dietrich, M.H. / Chan, L.J. / Adair, A. / Keremane, S. / Pymm, P. / Lo, A.W. / Cao, Y.C. / Tham, W.H.
History
DepositionOct 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Surface protein P12p
A: Surface protein P12p


Theoretical massNumber of molelcules
Total (without water)74,4952
Polymers74,4952
Non-polymers00
Water18010
1
B: Surface protein P12p


Theoretical massNumber of molelcules
Total (without water)37,2471
Polymers37,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Surface protein P12p


Theoretical massNumber of molelcules
Total (without water)37,2471
Polymers37,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.999, 74.175, 183.929
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Surface protein P12p /


Mass: 37247.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: PFS12P, PF12P, PFF0620c / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: C6KSX1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.38 Å3/Da / Density % sol: 48.34 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 2.5% MPD, 0.02 M alanine, 0.1 M bicine-tris pH 8.5, 0.02 M glycine, 0.02 M lysine, 12.5% PEG1000, 12.5% PEG3350, 0.02 M serine, 0.02M sodium glutamate, 0.2 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953647 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953647 Å / Relative weight: 1
ReflectionResolution: 2.79→47.257 Å / Num. obs: 18315 / % possible obs: 99.7 % / Redundancy: 7.362 % / Biso Wilson estimate: 63.124 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.183 / Rrim(I) all: 0.197 / Χ2: 0.945 / Net I/σ(I): 8.44 / Num. measured all: 134842
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2% possible allRrim(I) all
2.79-2.967.2081.4841.1428800.71798.8
2.96-3.177.2530.9271.9827030.8421000.999
3.17-3.427.8070.5123.7125760.9491000.547
3.42-3.747.6640.2686.6523710.9861000.287
3.74-4.187.4080.16710.0521240.9951000.18
4.18-4.827.0120.10714.619190.9961000.115
4.82-5.897.670.09917.1416450.99599.90.106
5.89-8.277.0660.09916.713060.9951000.107
8.27-47.2576.5260.05726.947910.996990.062

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.15_3459refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YMO

2ymo


Resolution: 2.8→47.257 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 34.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2948 911 5 %
Rwork0.2502 17305 -
obs0.2526 18216 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.15 Å2 / Biso mean: 69.355 Å2 / Biso min: 31.51 Å2
Refinement stepCycle: final / Resolution: 2.8→47.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4060 0 0 10 4070
Biso mean---66.18 -
Num. residues----525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034178
X-RAY DIFFRACTIONf_angle_d0.6255681
X-RAY DIFFRACTIONf_dihedral_angle_d6.6793373
X-RAY DIFFRACTIONf_chiral_restr0.049636
X-RAY DIFFRACTIONf_plane_restr0.004742
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.8-2.94770.40461280.36912420
2.9477-3.13230.3971270.34762417
3.1323-3.37410.3461280.2832440
3.3741-3.71350.26551290.25892453
3.7135-4.25060.28871300.22482452
4.2506-5.35410.24431310.20152500
5.3541-47.2570.29641380.24942623

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