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- PDB-3s62: Structure of Fab fragment of malaria transmission blocking antibo... -

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Basic information

Entry
Database: PDB / ID: 3s62
TitleStructure of Fab fragment of malaria transmission blocking antibody 2A8 against P. vivax P25 protein
Components
  • Fab fragment of antibody 2A8, Heavy chain
  • Fab fragment of antibody 2A8, Light chain
KeywordsIMMUNE SYSTEM / typical antibody fold
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.01 Å
AuthorsSaxena, A.K.
CitationJournal: Int.J.Biol.Macromol. / Year: 2012
Title: Structure of Fab fragment of malaria transmission blocking antibody 2A8 against P. vivax P25 protein
Authors: Saxena, A.K.
History
DepositionMay 24, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Fab fragment of antibody 2A8, Light chain
H: Fab fragment of antibody 2A8, Heavy chain


Theoretical massNumber of molelcules
Total (without water)46,3972
Polymers46,3972
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-17 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.075, 177.819, 74.624
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: Antibody Fab fragment of antibody 2A8, Light chain


Mass: 23282.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Tissue: Ascites fluid
#2: Antibody Fab fragment of antibody 2A8, Heavy chain


Mass: 23113.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Tissue: Ascites fluid
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: 4.79 Å3/Da / Density % sol: 74.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES, 25% PEGMME550, 10mM ZnSO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 14, 2004
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→100 Å / Num. all: 7804 / Num. obs: 7444 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rsym value: 0.15 / Net I/σ(I): 13.2
Reflection shellHighest resolution: 4.009 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 13.2 / Num. unique all: 7444 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z3G

1z3g


Resolution: 4.01→50 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.87 / SU B: 55.388 / SU ML: 0.73 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.834 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31001 524 4.6 %RANDOM
Rwork0.26441 ---
all0.26646 7804 --
obs0.26646 7444 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 100.907 Å2
Baniso -1Baniso -2Baniso -3
1--11.34 Å20 Å20 Å2
2---0.69 Å20 Å2
3---12.02 Å2
Refinement stepCycle: LAST / Resolution: 4.01→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3231 0 0 0 3231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223328
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.9434540
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.815425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.34124.463121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.59415527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.339159
X-RAY DIFFRACTIONr_chiral_restr0.1130.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212489
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.441.52131
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.82723460
X-RAY DIFFRACTIONr_scbond_it0.85131197
X-RAY DIFFRACTIONr_scangle_it1.5874.51080
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4.009→4.113 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 31 -
Rwork0.335 524 -
obs-524 98.58 %

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