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- PDB-3hfm: STRUCTURE OF AN ANTIBODY-ANTIGEN COMPLEX. CRYSTAL STRUCTURE OF TH... -

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Basic information

Entry
Database: PDB / ID: 3hfm
TitleSTRUCTURE OF AN ANTIBODY-ANTIGEN COMPLEX. CRYSTAL STRUCTURE OF THE HY/HEL-10 FAB-LYSOZYME COMPLEX
Components
  • HEN EGG WHITE LYSOZYME
  • HYHEL-10 IGG1 FAB (HEAVY CHAIN)
  • HYHEL-10 IGG1 FAB (LIGHT CHAIN)
KeywordsCOMPLEX(ANTIBODY-ANTIGEN)
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / 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 / endoplasmic reticulum / extracellular space / identical protein binding / 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-like domain superfamily ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsPadlan, E.A. / Davies, D.R.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1989
Title: Structure of an antibody-antigen complex: crystal structure of the HyHEL-10 Fab-lysozyme complex.
Authors: Padlan, E.A. / Silverton, E.W. / Sheriff, S. / Cohen, G.H. / Smith-Gill, S.J. / Davies, D.R.
#1: Journal: J.Mol.Biol. / Year: 1987
Title: A Three-Dimensional Model of an Anti-Lysozyme Antibody
Authors: Smith-Gill, S.J. / Mainhart, C. / Lavoie, T.B. / Feldmann, R.J. / Drohan, W. / Brooks, B.R.
#2: Journal: J.Mol.Biol. / Year: 1984
Title: Crystalline Monoclonal Antibody Fabs Complexed to Hen Egg White Lysozyme
Authors: Silverton, E.W. / Padlan, E.A. / Davies, D.R. / Smith-Gill, S. / Potter, M.
History
DepositionAug 11, 1988Processing site: BNL
Revision 1.0Jul 12, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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
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_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id
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: HYHEL-10 IGG1 FAB (LIGHT CHAIN)
H: HYHEL-10 IGG1 FAB (HEAVY CHAIN)
Y: HEN EGG WHITE LYSOZYME


Theoretical massNumber of molelcules
Total (without water)61,2073
Polymers61,2073
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.468, 118.734, 137.678
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES PRO L 8, PRO L 95, PRO L 141, PRO H 147, PRO H 149 AND PRO H 187 ARE CIS-PROLINES.

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Components

#1: Antibody HYHEL-10 IGG1 FAB (LIGHT CHAIN)


Mass: 23552.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
#2: Antibody HYHEL-10 IGG1 FAB (HEAVY CHAIN)


Mass: 23322.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
#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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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

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Sample preparation

CrystalDensity Matthews: 3.84 Å3/Da / Density % sol: 67.93 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: referred to J.Mol.Biol. 180.761-765 1984
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlHyHEL-10Fab1drop
20.01 Mcacodylate1drop
310 %PEG40001reservoir
415 %MPD1reservoir
50.1 Mimidazole1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / Num. obs: 12501 / % possible obs: 78 % / Observed criterion σ(F): 3 / Rmerge(I) obs: 0.066

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 3→10 Å / Rfactor obs: 0.246
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4296 0 0 1 4297
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.3
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor obs: 0.24 / Highest resolution: 3 Å / Lowest resolution: 10 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d0.034
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_deg

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