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- PDB-1qbl: FAB E8 (FABE8A) X-RAY STRUCTURE AT 2.26 ANGSTROM RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1qbl
TitleFAB E8 (FABE8A) X-RAY STRUCTURE AT 2.26 ANGSTROM RESOLUTION
Components(FABE8A) x 2
KeywordsIMMUNOGLOBULIN / IGG1 KAPPA / ANTIBODY / FAB FRAGMENT / ANTI-CYTOCHROME C ANTIBODY
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Immunoglobulin kappa chain variable 12-41
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsMylvaganam, S.E. / Paterson, Y. / Getzoff, E.D.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Structural basis for the binding of an anti-cytochrome c antibody to its antigen: crystal structures of FabE8-cytochrome c complex to 1.8 A resolution and FabE8 to 2.26 A resolution.
Authors: Mylvaganam, S.E. / Paterson, Y. / Getzoff, E.D.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Biochemical Implications from the Variable Gene Sequences of an Anti-Cytochrome C Antibody and Crystallographic Characterization of its Antigen-Binding Fragment in Free and Antigen-Complexed Forms
Authors: Mylvaganam, S.E. / Paterson, Y. / Kaiser, K. / Bowdish, K. / Getzoff, E.D.
#2: Journal: J.Immunol. / Year: 1985
Title: Monoclonal Antibodies to Horse Cytochrome C Expressing Four Distinct Idiotypes Distribute Among Two Sites on the Native Protein
Authors: Carbone, F.R. / Paterson, Y.
History
DepositionApr 29, 1998Processing site: BNL
Revision 1.0Dec 2, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 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: FABE8A
H: FABE8A


Theoretical massNumber of molelcules
Total (without water)47,1742
Polymers47,1742
Non-polymers00
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-25 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.840, 82.330, 64.520
Angle α, β, γ (deg.)90.00, 104.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody FABE8A / FAB E8


Mass: 23655.057 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Details: E8 ANTIBODY PURIFIED FROM ASCITES / Source: (natural) Mus musculus (house mouse) / Cell line: P3-X63-AG8.653 / Organ: SPLEEN / Strain: BALB/C / References: UniProt: P01635
#2: Antibody FABE8A / FAB E8


Mass: 23519.238 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Details: E8 ANTIBODY PURIFIED FROM ASCITES / Source: (natural) Mus musculus (house mouse) / Cell line: P3-X63-AG8.653 / Organ: SPLEEN / Strain: BALB/C / References: PIR: S49220
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.2 Å3/Da / Density % sol: 43 %
Crystal growpH: 6.2
Details: 0.05M SODIUM AMMONIUM PHOSPHATE BUFFER, PH 6.2, 25% (W/V) PEG 4000.
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.05 Msodium ammonium1reservoir
220 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 2.26
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 4, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.26 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 21365 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 32.7 Å2 / Rsym value: 0.073 / Net I/σ(I): 26.2
Reflection shellResolution: 2.26→2.36 Å / Mean I/σ(I) obs: 8 / Rsym value: 0.23 / % possible all: 99.7
Reflection
*PLUS
Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 99.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1.9 A RESOLUTION FAB J539

Resolution: 2.26→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.277 -10 %
Rwork0.192 --
obs0.192 21085 99.8 %
Displacement parametersBiso mean: 36.8 Å2
Baniso -1Baniso -3Baniso -2
1-10.352 Å24.192 Å2-
2---3.69 Å2
3--3.613 Å2-
Refine analyze
ObsFree
Luzzati d res low20 Å-
Luzzati sigma a0.31 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.26→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3318 0 0 331 3649
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.67
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.26→2.36 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3455 -10.4 %
Rwork0.4094 2354 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1
X-RAY DIFFRACTION2PARHCSDXB.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.6
LS refinement shell
*PLUS
Rfactor obs: 0.4094

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