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- PDB-6yhq: Crystal Structure of Fab F5.18.6, anti-Plasmodium vivax AMA1 -

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Basic information

Entry
Database: PDB / ID: 6yhq
TitleCrystal Structure of Fab F5.18.6, anti-Plasmodium vivax AMA1
Components
  • Fab F5.18.6 anti-Plasmodium vivax AMA1, heavy chain
  • Fab F5.18.6 anti-Plasmodium vivax AMA1, kappa light chain
KeywordsIMMUNE SYSTEM / immunoglobulin / Fab / Malaria / AMA1 / Plasmodium
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / THIOCYANATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsBentley, G.A. / Saul, F.A. / Vulliez-le Normand, B.
CitationJournal: To Be Published
Title: Crystal Structure of Fab F5.18.6, anti-Plasmodium vivax AMA1
Authors: Bentley, G.A. / Saul, F.A. / Vulliez-le Normand, B.
History
DepositionMar 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Fab F5.18.6 anti-Plasmodium vivax AMA1, heavy chain
L: Fab F5.18.6 anti-Plasmodium vivax AMA1, kappa light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6004
Polymers46,4772
Non-polymers1232
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-57 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.080, 114.990, 40.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Antibody Fab F5.18.6 anti-Plasmodium vivax AMA1, heavy chain


Mass: 23616.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Fab F5.18.6 anti-Plasmodium vivax AMA1, kappa light chain


Mass: 22860.232 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.23 Å3/Da / Density % sol: 61.9 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.18M KSCN, 16% PEG4000, 0.005M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Dec 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.89→73.32 Å / Num. obs: 36659 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.053 / Rrim(I) all: 0.142 / Net I/σ(I): 9.9
Reflection shellResolution: 1.89→1.99 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.858 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5255 / CC1/2: 0.415 / Rpim(I) all: 0.381 / Rrim(I) all: 0.942 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (3-OCT-2019)refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CLO, 1QKZ

1clo

1qkz


Resolution: 1.89→36 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.905 / SU R Cruickshank DPI: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.159 / SU Rfree Blow DPI: 0.15 / SU Rfree Cruickshank DPI: 0.142
RfactorNum. reflection% reflectionSelection details
Rfree0.2387 1480 4.05 %RANDOM
Rwork0.1851 ---
obs0.1872 36579 99.9 %-
Displacement parametersBiso max: 84.13 Å2 / Biso mean: 29.03 Å2 / Biso min: 11.57 Å2
Baniso -1Baniso -2Baniso -3
1-6.8558 Å20 Å20 Å2
2---1.2791 Å20 Å2
3----5.5767 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 1.89→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3210 0 4 432 3646
Biso mean--38.5 39.03 -
Num. residues----423
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1072SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes549HARMONIC5
X-RAY DIFFRACTIONt_it3307HARMONIC10
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion440SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2897SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3307HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg4508HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion3.84
X-RAY DIFFRACTIONt_other_torsion15.96
LS refinement shellResolution: 1.89→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3053 35 4.78 %
Rwork0.2426 697 -
all0.2454 732 -
obs--99.32 %

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