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- PDB-7kji: Plasmodium falciparum protein Pf12p bound to nanobody D9 -

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Basic information

Entry
Database: PDB / ID: 7kji
TitlePlasmodium falciparum protein Pf12p bound to nanobody D9
Components
  • Nanobody D9
  • Surface protein P12p
KeywordsUNKNOWN FUNCTION / Plasmodium falciparum / 6-cysteine protein / s48/45 domain / nanobody
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 speciesVicugna pacos (alpaca)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 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
A: Nanobody D9
B: Surface protein P12p


Theoretical massNumber of molelcules
Total (without water)50,8902
Polymers50,8902
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-6 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.991, 67.098, 110.945
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: Antibody Nanobody D9


Mass: 13642.261 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#2: Protein Surface protein P12p /


Mass: 37247.488 Da / Num. of mol.: 1
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

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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: 2.27 Å3/Da / Density % sol: 45.74 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M bis-tris chloride pH 6.5, 0.2 M magnesium chloride, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953649 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953649 Å / Relative weight: 1
ReflectionResolution: 3.25→42.753 Å / Num. obs: 7710 / % possible obs: 99.8 % / Redundancy: 13.102 % / Biso Wilson estimate: 99.233 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.153 / Rrim(I) all: 0.16 / Χ2: 0.764 / Net I/σ(I): 13.51 / Num. measured all: 101019
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
3.25-3.4412.9782.0181.4415665121612070.7412.199.3
3.44-3.6812.8980.9693.0814652113711360.9151.00999.9
3.68-3.9713.8960.5445.4314994107910790.9670.564100
3.97-4.3513.7690.25210.81136049889880.9920.262100
4.35-4.8613.2030.13917.16119229039030.9960.145100
4.86-5.612.4650.11220.41100728088080.9970.116100
5.6-6.8313.590.10323.2893776906900.9980.107100
6.83-9.5512.5460.0633469385535530.9990.065100
9.55-42.75310.9680.04844.7737953493460.9990.0599.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.15_3459refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KJ7

7kj7


Resolution: 3.25→42.753 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2855 1540 20.02 %
Rwork0.2452 6151 -
obs0.2534 7691 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.91 Å2 / Biso mean: 110.5409 Å2 / Biso min: 69.41 Å2
Refinement stepCycle: final / Resolution: 3.25→42.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2756 0 0 0 2756
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032821
X-RAY DIFFRACTIONf_angle_d0.5783847
X-RAY DIFFRACTIONf_dihedral_angle_d9.1971636
X-RAY DIFFRACTIONf_chiral_restr0.049431
X-RAY DIFFRACTIONf_plane_restr0.004507
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.2502-3.3550.38181370.3375548
3.355-3.47490.36061340.3263534
3.4749-3.6140.41951370.2955550
3.614-3.77830.35531390.2887552
3.7783-3.97740.31221380.2913553
3.9774-4.22640.25491360.237545
4.2264-4.55240.27971390.214556
4.5524-5.00990.24031390.1829557
5.0099-5.73330.26571430.2367569
5.7333-7.21780.30121440.2679576
7.2178-42.7530.261540.236611

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