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- PDB-4py7: Crystal Structure of Fab 3.1 -

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Basic information

Entry
Database: PDB / ID: 4py7
TitleCrystal Structure of Fab 3.1
Components
  • antibody 3.1 heavy chain
  • antibody 3.1 light chain
KeywordsIMMUNE SYSTEM / immunoglobulin Fab fragment / neutralizing antibody / hemagglutinin glycoproteins
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDreyfus, C.
CitationJournal: J.Virol. / Year: 2014
Title: Alternative Recognition of the Conserved Stem Epitope in Influenza A Virus Hemagglutinin by a VH3-30-Encoded Heterosubtypic Antibody.
Authors: Wyrzucki, A. / Dreyfus, C. / Kohler, I. / Steck, M. / Wilson, I.A. / Hangartner, L.
History
DepositionMar 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
I: antibody 3.1 heavy chain
J: antibody 3.1 light chain
A: antibody 3.1 heavy chain
B: antibody 3.1 light chain


Theoretical massNumber of molelcules
Total (without water)93,5274
Polymers93,5274
Non-polymers00
Water00
1
I: antibody 3.1 heavy chain
J: antibody 3.1 light chain


Theoretical massNumber of molelcules
Total (without water)46,7632
Polymers46,7632
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-26 kcal/mol
Surface area19510 Å2
MethodPISA
2
A: antibody 3.1 heavy chain
B: antibody 3.1 light chain


Theoretical massNumber of molelcules
Total (without water)46,7632
Polymers46,7632
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-26 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.842, 73.842, 207.954
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Antibody antibody 3.1 heavy chain


Mass: 23603.652 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody antibody 3.1 light chain


Mass: 23159.715 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
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: 3.03 Å3/Da / Density % sol: 59.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M calcium acetate, 10% PEG8000, 100 mM Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 75 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.71941 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2011
RadiationMonochromator: double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.71941 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 30297 / Num. obs: 30297 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.7→2.75 Å / % possible all: 98.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.881 / SU B: 14.868 / SU ML: 0.299 / Cross valid method: THROUGHOUT / ESU R: 1.029 / ESU R Free: 0.36 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2727 1521 5.1 %RANDOM
Rwork0.22762 ---
obs0.22998 28423 98.13 %-
all-29944 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.001 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2---0.59 Å20 Å2
3---1.19 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6498 0 0 0 6498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226654
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.9519056
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3145849
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.13723.969262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.082151055
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8331532
X-RAY DIFFRACTIONr_chiral_restr0.0980.21023
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215012
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_it0.6261.54249
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20326870
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.46432405
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5534.52186
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.452 116 -
Rwork0.348 2117 -
obs--98.81 %

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