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- PDB-2iq9: PFA2 FAB fragment, triclinic apo form -

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Basic information

Entry
Database: PDB / ID: 2iq9
TitlePFA2 FAB fragment, triclinic apo form
Components
  • IgG2a Fab fragment PFA2 Kappa light chain
  • IgG2a Fab fragment PFA2 heavy chain
KeywordsIMMUNE SYSTEM / pfa2 / wwddd / cdr
Function / homology
Function and homology information


: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETAMIDE / If kappa light chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGardberg, A.S. / Dealwis, C.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Molecular basis for passive immunotherapy of Alzheimer's disease
Authors: Gardberg, A.S. / Dice, L.T. / Ou, S. / Rich, R.L. / Helmbrecht, E. / Ko, J. / Wetzel, R. / Myszka, D.G. / Patterson, P.H. / Dealwis, C.
History
DepositionOct 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE Presently, there is no aminoacid sequence database reference available for the two ...SEQUENCE Presently, there is no aminoacid sequence database reference available for the two proteins IGG2A FAB fragment heavy chain and IGG2A FAB fragment light chain kappa

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IgG2a Fab fragment PFA2 Kappa light chain
H: IgG2a Fab fragment PFA2 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1694
Polymers48,0512
Non-polymers1182
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-21 kcal/mol
Surface area19590 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)41.564, 42.776, 58.355
Angle α, β, γ (deg.)95.81, 94.81, 91.11
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a heterodimer.

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Components

#1: Antibody IgG2a Fab fragment PFA2 Kappa light chain


Mass: 24146.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c / References: UniProt: A2NHM3*PLUS
#2: Antibody IgG2a Fab fragment PFA2 heavy chain


Mass: 23903.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c
#3: Chemical ChemComp-ACM / ACETAMIDE


Mass: 59.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.49 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 8.5
Details: 25% PEG3350, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 12, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→22 Å / Num. obs: 16504 / % possible obs: 93.3 % / Redundancy: 1.7 % / Biso Wilson estimate: 38.6 Å2 / Rsym value: 0.072 / Net I/σ(I): 10.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2 / Num. unique all: 1639 / Rsym value: 0.359 / % possible all: 92.8

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NCW

1ncw


Resolution: 2.3→20.7 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.9 / SU B: 10.855 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.79 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.278 854 5.2 %RANDOM
Rwork0.211 ---
obs0.215 16487 93.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.147 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.03 Å20.02 Å2
2---0.02 Å20.12 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3362 0 8 165 3535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223469
X-RAY DIFFRACTIONr_bond_other_d0.0010.022312
X-RAY DIFFRACTIONr_angle_refined_deg1.3321.9564734
X-RAY DIFFRACTIONr_angle_other_deg0.8443.0035658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5835443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95124.122131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.40815554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6091514
X-RAY DIFFRACTIONr_chiral_restr0.0760.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023846
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02681
X-RAY DIFFRACTIONr_nbd_refined0.1810.2637
X-RAY DIFFRACTIONr_nbd_other0.1960.22356
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21584
X-RAY DIFFRACTIONr_nbtor_other0.0840.21918
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2164
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0350.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2370.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.219
X-RAY DIFFRACTIONr_mcbond_it0.6161.52266
X-RAY DIFFRACTIONr_mcbond_other0.0861.5889
X-RAY DIFFRACTIONr_mcangle_it1.05923575
X-RAY DIFFRACTIONr_scbond_it1.06331423
X-RAY DIFFRACTIONr_scangle_it1.6074.51156
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 60 -
Rwork0.293 1137 -
obs-1197 92.36 %

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