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- PDB-2iff: STRUCTURE OF AN ANTIBODY-LYSOZYME COMPLEX: EFFECT OF A CONSERVATI... -

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Basic information

Entry
Database: PDB / ID: 2iff
TitleSTRUCTURE OF AN ANTIBODY-LYSOZYME COMPLEX: EFFECT OF A CONSERVATIVE MUTATION
Components
  • HEN EGG WHITE LYSOZYME
  • IGG1 HYHEL-5 FAB (HEAVY CHAIN)
  • IGG1 HYHEL-5 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN/HYDROLASE(O-GLYCOSYL) / IMMUNOGLOBULIN-HYDROLASE(O-GLYCOSYL) complex
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: 2.65 Å
AuthorsChacko, S. / Davies, D.R.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Structure of an antibody-lysozyme complex unexpected effect of conservative mutation.
Authors: Chacko, S. / Silverton, E. / Kam-Morgan, L. / Smith-Gill, S. / Cohen, G. / Davies, D.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987
Title: Three-Dimensional Structure of an Antibody-Antigen Complex
Authors: Sheriff, S. / Silverton, E.W. / Padlan, E.A. / Cohen, G.H. / Smith-Gill, S.J. / Finzel, B.C. / Davies, D.R.
History
DepositionFeb 3, 1994Processing site: BNL
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 10, 2011Group: Structure summary
Revision 1.4Jun 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 / 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_ref_seq_dif.details
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGG1 HYHEL-5 FAB (LIGHT CHAIN)
H: IGG1 HYHEL-5 FAB (HEAVY CHAIN)
Y: HEN EGG WHITE LYSOZYME


Theoretical massNumber of molelcules
Total (without water)60,6053
Polymers60,6053
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.800, 74.800, 79.000
Angle α, β, γ (deg.)90.00, 101.80, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO L 8 / 2: CIS PROLINE - PRO L 139 / 3: CIS PROLINE - PRO H 150 / 4: CIS PROLINE - PRO H 152 / 5: CIS PROLINE - PRO H 192

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Components

#1: Antibody IGG1 HYHEL-5 FAB (LIGHT CHAIN)


Mass: 23326.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 1042224
#2: Antibody IGG1 HYHEL-5 FAB (HEAVY CHAIN)


Mass: 22975.445 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: 14303.146 Da / Num. of mol.: 1 / Mutation: R68K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00698
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE LIGHT CHAIN OF THE FAB HAS CHAIN INDICATOR L. THE HEAVY CHAIN OF THE FAB HAS CHAIN INDICATOR H. ...THE LIGHT CHAIN OF THE FAB HAS CHAIN INDICATOR L. THE HEAVY CHAIN OF THE FAB HAS CHAIN INDICATOR H. THE LYSOZYME HAS CHAIN INDICATOR Y. THE NUMBERING SYSTEM USED IN THIS ENTRY IS SEQUENTIAL, FROM 1 - 212 FOR THE LIGHT CHAIN AND FROM 1 - 215 FOR THE HEAVY CHAIN. THE CONVERSION TO KABAT NUMBERING (E.A. KABAT, T.T. WU, M. REID-MILLER, H.M. PERRY, K.S. GOTTESMAN (1991) SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST, 5TH ED, NATIONAL INSTITUTES OF HEALTH, BETHESDA, MD) FOR THE VARIABLE REGIONS OF THE LIGHT AND HEAVY CHAINS IS GIVEN BELOW. THE NUMBERING SYSTEM USED IS THE SAME AS IN THE PDB COORDINATE FILE FOR THE WILD-TYPE HYHEL-5-LYSOZYME COMPLEX. SEQUENTIAL NUMBERING KABAT NUMBERING L1 - L27 1 - 27 L28 - L94 29 - 95 L95 - L106 97 - 108 H2 - H52 2 - 52 H53 52A H54 - H83 53 - 82 H84 - H86 82A - 82C H87 - H102 83 - 98 H103 - H116 100 - 113 RESIDUE 84 IN THE LIGHT CHAIN WAS IDENTIFIED AS A GLUTAMATE IN THE WILD-TYPE STRUCTURE (SHERIFF ET AL., 1987). THIS RESIDUE HAS NOW BEEN SHOWN TO BE A THREONINE (M.A NEWMAN AND S.J. SMITH-GILL, PERSONAL COMMUNICATION) AND THIS STRUCTURE REFLECTS THE CHANGE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 52.97 %
Crystal grow
*PLUS
pH: 7.2 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 MFab11
21.2 Mprotein11
312 %(v/v)PEG400012
40.1 Mimidazole12
58 mMspermine12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 9999 Å / Num. obs: 12909 / % possible obs: 66.4 % / Num. measured all: 37251 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.76 Å / % possible obs: 22.3 % / Num. unique obs: 717 / Num. measured obs: 1140 / Mean I/σ(I) obs: 3.82

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.65→10 Å / σ(F): 2 /
Num. reflection% reflection
obs12336 69.2 %
Refinement stepCycle: LAST / Resolution: 2.65→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4241 0 0 80 4321
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg3.01
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
Rfactor obs: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg27.7
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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