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- PDB-2q76: Mouse anti-hen egg white lysozyme antibody F10.6.6 Fab fragment -

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Basic information

Entry
Database: PDB / ID: 2q76
TitleMouse anti-hen egg white lysozyme antibody F10.6.6 Fab fragment
Components
  • Fab F10.6.6 fragment Heavy Chain
  • Fab F10.6.6 fragment Light Chain
KeywordsIMMUNE SYSTEM / Antibody / Fab fragment / lysozyme / affinity maturation / VH-VL interface.
Function / homology
Function and homology information


IgG immunoglobulin complex / B cell differentiation / extracellular region / plasma membrane
Similarity search - Function
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/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
Immunoglobulin kappa constant
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCauerhff, A. / Klinke, S. / Acierno, J.P. / Goldbaum, F.A. / Braden, B.C.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Affinity maturation increases the stability and plasticity of the Fv domain of anti-protein antibodies.
Authors: Acierno, J.P. / Braden, B.C. / Klinke, S. / Goldbaum, F.A. / Cauerhff, A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Structural mechanism for affinity maturation of an anti-lysozyme antibody
Authors: Cauerhff, A. / Goldbaum, F.A. / Braden, B.C.
History
DepositionJun 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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
Remark 999sequence The sequences for Fab F10.6.6 fragment Light and heavy chains are not in the UNP database ...sequence The sequences for Fab F10.6.6 fragment Light and heavy chains are not in the UNP database at the time of processing. Author indicated the sequence references AF110316.3 GI:32456055 for VH, and AY277254.1 GI:33642144 for VL, respectively. Both sequences are identical to the sequences in the coordinates.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fab F10.6.6 fragment Light Chain
B: Fab F10.6.6 fragment Heavy Chain
C: Fab F10.6.6 fragment Light Chain
D: Fab F10.6.6 fragment Heavy Chain


Theoretical massNumber of molelcules
Total (without water)93,0394
Polymers93,0394
Non-polymers00
Water9,314517
1
A: Fab F10.6.6 fragment Light Chain
B: Fab F10.6.6 fragment Heavy Chain


Theoretical massNumber of molelcules
Total (without water)46,5192
Polymers46,5192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Fab F10.6.6 fragment Light Chain
D: Fab F10.6.6 fragment Heavy Chain


Theoretical massNumber of molelcules
Total (without water)46,5192
Polymers46,5192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.760, 80.250, 91.500
Angle α, β, γ (deg.)90.00, 91.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Fab F10.6.6 fragment Light Chain


Mass: 23320.539 Da / Num. of mol.: 2 / Fragment: domain VL and CL / Source method: isolated from a natural source
Details: The antibody was obtained from ascitic fluid generated by injecting monoclonal hybridoma cells.
Source: (natural) Mus musculus (house mouse) / Strain: BALB/c / References: UniProt: P01837*PLUS
#2: Antibody Fab F10.6.6 fragment Heavy Chain


Mass: 23198.896 Da / Num. of mol.: 2 / Fragment: domain VH and CH1 / Source method: isolated from a natural source
Details: The antibody was obtained from ascitic fluid generated by injecting monoclonal hybridoma cells.
Source: (natural) Mus musculus (house mouse) / Strain: BALB/c
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 517 / Source method: isolated from a natural source / Formula: H2O

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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: 42.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: The F10.6.6 Fab fragment was crystallized in a mother liquor containing 24% (w/v) PEG 1000, 0.2 M CaCl2 and 0.1 M acetate buffer pH 4.7. Large prisms of about 0.30 mm x 0.05 mm x 0.05 mm ...Details: The F10.6.6 Fab fragment was crystallized in a mother liquor containing 24% (w/v) PEG 1000, 0.2 M CaCl2 and 0.1 M acetate buffer pH 4.7. Large prisms of about 0.30 mm x 0.05 mm x 0.05 mm were obtained after several weeks. VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 4.70

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.431 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 14, 2003
RadiationMonochromator: SI SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.431 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 50300 / Num. obs: 50300 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 9.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 3.3 / Num. unique all: 7122 / Rsym value: 0.195 / % possible all: 92

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Processing

Software
NameClassification
MAR345dtbdata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Fab fragment of PDB 1P2C

1p2c


Resolution: 2→50 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.233 4403
Rwork0.196 -
obs0.198 47530
all-50300
Displacement parametersBiso mean: 22 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6484 0 0 517 7001
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.41
X-RAY DIFFRACTIONc_bond_d0.006

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