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- PDB-8rek: Plasmodium vivax Apical Membrane Antigen 1/Fab complex -

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Basic information

Entry
Database: PDB / ID: 8rek
TitlePlasmodium vivax Apical Membrane Antigen 1/Fab complex
Components
  • Apical membrane antigen 1 (Fragment)
  • Fab 8.1.1 heavy chain
  • Fab 8.1.1 light chain
KeywordsIMMUNE SYSTEM / AMA-1 / Plasmodium vivax / Antigen / Fab
Function / homologyApical membrane antigen 1 domain superfamily / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / membrane / Apical membrane antigen 1
Function and homology information
Biological speciesPlasmodium vivax Sal-1 (eukaryote)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsBentley, G.A. / Saul, F.A. / Vulliez-LeNormand, B.
Funding support France, 1items
OrganizationGrant numberCountry
Other private France
CitationJournal: J Struct Biol X / Year: 2024
Title: Conformational variability in the D2 loop of Plasmodium Apical Membrane antigen 1.
Authors: Saul, F.A. / Vulliez-Le Normand, B. / Boes, A. / Spiegel, H. / Kocken, C.H.M. / Faber, B.W. / Bentley, G.A.
History
DepositionDec 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apical membrane antigen 1 (Fragment)
H: Fab 8.1.1 heavy chain
L: Fab 8.1.1 light chain


Theoretical massNumber of molelcules
Total (without water)101,0173
Polymers101,0173
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-28 kcal/mol
Surface area37440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.390, 214.680, 57.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Apical membrane antigen 1 (Fragment)


Mass: 54180.820 Da / Num. of mol.: 1
Mutation: S178N, N226D, N441Q are potential N-glycosylation sites
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax Sal-1 (eukaryote) / Gene: AMA-1 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q9TY14
#2: Antibody Fab 8.1.1 heavy chain


Mass: 23539.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody Fab 8.1.1 light chain


Mass: 23296.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
Has ligand of interestY
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Crystals were obtained by mixing 0.8 micro-L of PvAMA1-Fab complex with 0.2 micro-L of 15% 1,2,3 heptanetriol and 0.8 micro-L of reservoir buffer comprising 20% PEG 2000 monomethylether and ...Details: Crystals were obtained by mixing 0.8 micro-L of PvAMA1-Fab complex with 0.2 micro-L of 15% 1,2,3 heptanetriol and 0.8 micro-L of reservoir buffer comprising 20% PEG 2000 monomethylether and 0.1 M Tris pH 7. The final protein concentration was 3.2 mg/ml.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 27, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.05→73.39 Å / Num. obs: 18062 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.067 / Rrim(I) all: 0.181 / Χ2: 0.97 / Net I/σ(I): 11.8 / Num. measured all: 128197
Reflection shellResolution: 3.05→3.26 Å / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 1.203 / Num. measured all: 23088 / Num. unique obs: 3193 / CC1/2: 0.316 / Rpim(I) all: 0.48 / Rrim(I) all: 1.296 / Χ2: 0.94 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→69.54 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.866 / SU B: 68.08 / SU ML: 0.513 / Cross valid method: THROUGHOUT / ESU R Free: 0.551 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29202 946 5.3 %RANDOM
Rwork0.22134 ---
obs0.22508 17069 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 95.223 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å2-0 Å2
2--0.41 Å2-0 Å2
3---0.35 Å2
Refinement stepCycle: 1 / Resolution: 3.05→69.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6293 0 0 0 6293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0126450
X-RAY DIFFRACTIONr_bond_other_d0.0170.0165781
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.668770
X-RAY DIFFRACTIONr_angle_other_deg0.7871.57413361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6665807
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.302532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.615101015
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.2960
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027621
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021471
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6165.8733258
X-RAY DIFFRACTIONr_mcbond_other3.6155.8733258
X-RAY DIFFRACTIONr_mcangle_it5.81410.7154055
X-RAY DIFFRACTIONr_mcangle_other5.81810.7174056
X-RAY DIFFRACTIONr_scbond_it3.3466.0433192
X-RAY DIFFRACTIONr_scbond_other3.3466.0453193
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.54511.1444716
X-RAY DIFFRACTIONr_long_range_B_refined8.20555.096217
X-RAY DIFFRACTIONr_long_range_B_other8.20555.16218
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.05→3.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 71 -
Rwork0.381 1229 -
obs--100 %
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)
13.11911.1831-1.5274.484-1.46682.5960.0287-0.2144-0.31670.1223-0.07140.05140.13180.06360.04260.05770.0452-0.04630.0862-0.0320.0872-25.7772-11.386212.4774
22.90560.6867-0.02344.87221.02433.0472-0.1320.27430.2503-0.42750.1446-0.2525-0.39910.0885-0.01260.32790.06750.12730.22090.08210.1179-0.292826.7779-9.1975
31.77131.62970.16712.3986-0.47953.4987-0.03590.0450.1336-0.1954-0.1227-0.77430.21770.57570.15860.59290.11730.18460.38520.10350.986219.466153.1877-14.5111
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 474
2X-RAY DIFFRACTION2H1 - 114
3X-RAY DIFFRACTION2L1 - 107
4X-RAY DIFFRACTION3H115 - 213
5X-RAY DIFFRACTION3L108 - 211

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