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- PDB-1fbi: CRYSTAL STRUCTURE OF A CROSS-REACTION COMPLEX BETWEEN FAB F9.13.7... -

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Basic information

Entry
Database: PDB / ID: 1fbi
TitleCRYSTAL STRUCTURE OF A CROSS-REACTION COMPLEX BETWEEN FAB F9.13.7 AND GUINEA-FOWL LYSOZYME
Components
  • GUINEA FOWL LYSOZYME
  • IGG1 F9.13.7 FAB (HEAVY CHAIN)
  • IGG1 F9.13.7 FAB (LIGHT CHAIN)
KeywordsCOMPLEX (ANTIBODY/ANTIGEN) / COMPLEX (ANTIBODY-ANTIGEN) / COMPLEX (ANTIBODY-ANTIGEN) complex
Function / homology
Function and homology information


phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding ...phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding / positive regulation of phagocytosis / B cell differentiation / positive regulation of immune response / lysozyme / lysozyme activity / antibacterial humoral response / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / external side of plasma membrane / extracellular space / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
: / Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme ...: / Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Lysozyme C / Immunoglobulin kappa constant / Ig gamma-1 chain C region secreted form
Similarity search - Component
Biological speciesMus musculus (house mouse)
Numida meleagris (helmeted guineafowl)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsLescar, J. / Alzari, P.M.
Citation
Journal: J.Biol.Chem. / Year: 1995
Title: Crystal structure of a cross-reaction complex between Fab F9.13.7 and guinea fowl lysozyme.
Authors: Lescar, J. / Pellegrini, M. / Souchon, H. / Tello, D. / Poljak, R.J. / Peterson, N. / Greene, M. / Alzari, P.M.
#1: Journal: Protein Sci. / Year: 1994
Title: Crystal Structures of Pheasant and Guinea-Fowl Egg-White Lysozymes
Authors: Lescar, J. / Souchon, H. / Alzari, P.
#2: Journal: Proteins / Year: 1993
Title: Crystallization, Preliminary X-Ray Diffraction Study, and Crystal Packing of a Complex between Anti-Hen Lysozyme Antibody and Guinea-Fowl Lysozyme
Authors: Lescar, J. / Riottot, M.-M. / Souchon, H. / Chitarra, V. / Bentley, G. / Navaza, J. / Alzari, P. / Poljak, R.
History
DepositionJan 19, 1995Processing site: BNL
Revision 1.0Feb 27, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Nov 20, 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: IGG1 F9.13.7 FAB (LIGHT CHAIN)
H: IGG1 F9.13.7 FAB (HEAVY CHAIN)
X: GUINEA FOWL LYSOZYME
P: IGG1 F9.13.7 FAB (LIGHT CHAIN)
Q: IGG1 F9.13.7 FAB (HEAVY CHAIN)
Y: GUINEA FOWL LYSOZYME


Theoretical massNumber of molelcules
Total (without water)123,5946
Polymers123,5946
Non-polymers00
Water00
1
L: IGG1 F9.13.7 FAB (LIGHT CHAIN)
H: IGG1 F9.13.7 FAB (HEAVY CHAIN)
X: GUINEA FOWL LYSOZYME


Theoretical massNumber of molelcules
Total (without water)61,7973
Polymers61,7973
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
P: IGG1 F9.13.7 FAB (LIGHT CHAIN)
Q: IGG1 F9.13.7 FAB (HEAVY CHAIN)
Y: GUINEA FOWL LYSOZYME


Theoretical massNumber of molelcules
Total (without water)61,7973
Polymers61,7973
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.700, 195.500, 50.200
Angle α, β, γ (deg.)90.00, 108.50, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO L 95 / 2: CIS PROLINE - PRO L 141 / 3: CIS PROLINE - PRO H 156 / 4: CIS PROLINE - PRO H 158 / 5: CIS PROLINE - PRO H 198 / 6: CIS PROLINE - PRO P 95 / 7: CIS PROLINE - PRO P 141 / 8: CIS PROLINE - PRO Q 41 / 9: CIS PROLINE - PRO Q 156 / 10: CIS PROLINE - PRO Q 158 / 11: CIS PROLINE - PRO Q 198

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Components

#1: Antibody IGG1 F9.13.7 FAB (LIGHT CHAIN)


Mass: 23833.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P01837*PLUS
#2: Antibody IGG1 F9.13.7 FAB (HEAVY CHAIN)


Mass: 23634.373 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P01868
#3: Protein GUINEA FOWL LYSOZYME


Mass: 14329.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Numida meleagris (helmeted guineafowl) / References: UniProt: P00704, lysozyme
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.95 %
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 5.5 / Method: vapor diffusion, hanging drop
Details: Lescar, J., (1993) Proteins.Struct.,Funct., Genet., 15, 209.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %(w/v)PEG80001reservoir
20.04 %sodium azide1reservoir
30.1 Mpotassium phosphate1reservoir
410 mMmagnesium chloride1reservoir
53 %(v/v)2-propanol1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 28224 / % possible obs: 95 %
Reflection
*PLUS
Highest resolution: 3 Å / Num. obs: 30232 / Num. measured all: 111931 / Rmerge(I) obs: 0.14 / Rmerge F obs: 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3→7 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.19 -
obs0.19 23703
Refinement stepCycle: LAST / Resolution: 3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8521 0 0 0 8521
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_deg1.65
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refinement
*PLUS
σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.65

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