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- PDB-1fdl: CRYSTALLOGRAPHIC REFINEMENT OF THE THREE-DIMENSIONAL STRUCTURE OF... -

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Basic information

Entry
Database: PDB / ID: 1fdl
TitleCRYSTALLOGRAPHIC REFINEMENT OF THE THREE-DIMENSIONAL STRUCTURE OF THE FAB D1.3-LYSOZYME COMPLEX AT 2.5-ANGSTROMS RESOLUTION
Components
  • HEN EGG WHITE LYSOZYME
  • IGG1-KAPPA D1.3 FAB (HEAVY CHAIN)
  • IGG1-KAPPA D1.3 FAB (LIGHT CHAIN)
KeywordsCOMPLEX (ANTIBODY-ANTIGEN)
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 / phagocytosis, engulfment / immunoglobulin complex, circulating / immunoglobulin mediated immune response / complement activation, classical pathway / positive regulation of phagocytosis ...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 / phagocytosis, engulfment / immunoglobulin complex, circulating / immunoglobulin mediated immune response / complement activation, classical pathway / positive regulation of phagocytosis / antigen binding / B cell differentiation / Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / positive regulation of immune response / cell wall macromolecule catabolic process / antibacterial humoral response / lysozyme / lysozyme activity / 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 / endoplasmic reticulum / extracellular space / extracellular region / identical protein binding / 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)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsFischmann, T.O. / Poljak, R.J.
CitationJournal: J.Biol.Chem. / Year: 1991
Title: Crystallographic refinement of the three-dimensional structure of the FabD1.3-lysozyme complex at 2.5-A resolution.
Authors: Fischmann, T.O. / Bentley, G.A. / Bhat, T.N. / Boulot, G. / Mariuzza, R.A. / Phillips, S.E. / Tello, D. / Poljak, R.J.
History
DepositionAug 27, 1990Processing site: BNL
Revision 1.0Oct 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGG1-KAPPA D1.3 FAB (LIGHT CHAIN)
H: IGG1-KAPPA D1.3 FAB (HEAVY CHAIN)
Y: HEN EGG WHITE LYSOZYME


Theoretical massNumber of molelcules
Total (without water)61,4063
Polymers61,4063
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.000, 143.500, 49.300
Angle α, β, γ (deg.)90.00, 120.40, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES PRO L 8, PRO L 95, PRO L 141, PRO H 150, PRO H 152 AND PRO H 192 ARE CIS PROLINES.

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Components

#1: Antibody IGG1-KAPPA D1.3 FAB (LIGHT CHAIN)


Mass: 23677.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Organ: EGG / Production host: Escherichia coli (E. coli) / References: GenBank: 2072141, UniProt: P01837*PLUS
#2: Antibody IGG1-KAPPA D1.3 FAB (HEAVY CHAIN)


Mass: 23398.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Organ: EGG / Production host: Escherichia coli (E. coli) / References: UniProt: P01868*PLUS
#3: Protein HEN EGG WHITE LYSOZYME


Mass: 14331.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P00698, 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: 2.78 Å3/Da / Density % sol: 55.77 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop / Details: referred to J.Mol.Biol. 170.1055-1058 / PH range low: 7 / PH range high: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-15 mg/mlFabD1.3-HEL1drop
220-22.5 %(w/v)PEG60001reservoir
30.1 Mpotassium phosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 5.5 Å / Num. obs: 20475 / Num. measured all: 41026 / Rmerge(I) obs: 2.5

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementRfactor Rwork: 0.184 / Highest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4309 0 0 0 4309
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg3.3
Refinement
*PLUS
Highest resolution: 2.5 Å / Rfactor all: 0.195 / Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg

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