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- PDB-1mlc: MONOCLONAL ANTIBODY FAB D44.1 RAISED AGAINST CHICKEN EGG-WHITE LY... -

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Basic information

Entry
Database: PDB / ID: 1mlc
TitleMONOCLONAL ANTIBODY FAB D44.1 RAISED AGAINST CHICKEN EGG-WHITE LYSOZYME COMPLEXED WITH LYSOZYME
Components
  • HEN EGG WHITE LYSOZYME
  • IGG1-KAPPA D44.1 FAB (HEAVY CHAIN)
  • IGG1-KAPPA D44.1 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 / Lactose synthesis / Antimicrobial peptides / B cell differentiation / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / positive regulation of immune response / cell wall macromolecule catabolic process / 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 / 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
AuthorsBraden, B.C. / Souchon, H. / Eisele, J.-L. / Bentley, G.A. / Bhat, T.N. / Navaza, J. / Poljak, R.J.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Three-dimensional structures of the free and the antigen-complexed Fab from monoclonal anti-lysozyme antibody D44.1.
Authors: Braden, B.C. / Souchon, H. / Eisele, J.L. / Bentley, G.A. / Bhat, T.N. / Navaza, J. / Poljak, R.J.
#1: Journal: J.Mol.Biol. / Year: 1988
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Two Antigen-Antibody (Lysozyme-Fab) Complexes
Authors: Fischmann, T. / Souchon, H. / Riottot, M.-M. / Tello, D. / Poljak, R.J.
History
DepositionMar 10, 1995Processing site: BNL
Revision 1.0Jun 3, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: IGG1-KAPPA D44.1 FAB (LIGHT CHAIN)
B: IGG1-KAPPA D44.1 FAB (HEAVY CHAIN)
C: IGG1-KAPPA D44.1 FAB (LIGHT CHAIN)
D: IGG1-KAPPA D44.1 FAB (HEAVY CHAIN)
E: HEN EGG WHITE LYSOZYME
F: HEN EGG WHITE LYSOZYME


Theoretical massNumber of molelcules
Total (without water)122,3146
Polymers122,3146
Non-polymers00
Water3,783210
1
A: IGG1-KAPPA D44.1 FAB (LIGHT CHAIN)
B: IGG1-KAPPA D44.1 FAB (HEAVY CHAIN)
E: HEN EGG WHITE LYSOZYME


Theoretical massNumber of molelcules
Total (without water)61,1573
Polymers61,1573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: IGG1-KAPPA D44.1 FAB (LIGHT CHAIN)
D: IGG1-KAPPA D44.1 FAB (HEAVY CHAIN)
F: HEN EGG WHITE LYSOZYME


Theoretical massNumber of molelcules
Total (without water)61,1573
Polymers61,1573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.700, 167.300, 84.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO A 8 / 2: CIS PROLINE - PRO A 95 / 3: CIS PROLINE - PRO A 141 / 4: CIS PROLINE - PRO B 150 / 5: CIS PROLINE - PRO B 152 / 6: CIS PROLINE - PRO B 192 / 7: CIS PROLINE - PRO C 8 / 8: CIS PROLINE - PRO C 95 / 9: CIS PROLINE - PRO C 141 / 10: CIS PROLINE - PRO D 150 / 11: CIS PROLINE - PRO D 152 / 12: CIS PROLINE - PRO D 192

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Components

#1: Antibody IGG1-KAPPA D44.1 FAB (LIGHT CHAIN)


Mass: 23609.846 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-KAPPA D44.1 FAB (HEAVY CHAIN)


Mass: 23215.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P01868*PLUS
#3: Protein HEN EGG WHITE LYSOZYME


Mass: 14331.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P00698
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
Compound detailsVL RESIDUE SER 30 IS IN THE SECOND POSITION OF A II'-TYPE TURN. VL RESIDUE VAL 51 IS THE SECOND ...VL RESIDUE SER 30 IS IN THE SECOND POSITION OF A II'-TYPE TURN. VL RESIDUE VAL 51 IS THE SECOND RESIDUE (I+1) OF A MODIFIED GAMMA TURN (CLASS 3).
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: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
212 %(w/v)PEG40001drop
30.1 Mcitrate1drop

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 44729 / % possible obs: 94 % / Redundancy: 4 % / Rmerge(I) obs: 0.1
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. measured all: 165512 / Rmerge(I) obs: 0.104

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Processing

Software
NameClassification
XDSdata scaling
PROLSQrefinement
XDSdata reduction
RefinementResolution: 2.5→7 Å / σ(F): 2
Details: D44.1-HEL COMPLEX CRYSTALS HAVE TWO FAB-HEL COMPLEXES IN THE ASYMMETRIC UNIT. COMPLEX NUMBER 1 INCLUDES CHAIN A (VL AND CL DOMAINS), CHAIN B (VH AND CH1 DOMAINS) AND CHAIN E (HEL). COMPLEX ...Details: D44.1-HEL COMPLEX CRYSTALS HAVE TWO FAB-HEL COMPLEXES IN THE ASYMMETRIC UNIT. COMPLEX NUMBER 1 INCLUDES CHAIN A (VL AND CL DOMAINS), CHAIN B (VH AND CH1 DOMAINS) AND CHAIN E (HEL). COMPLEX NUMBER 2 INCLUDES CHAIN C (VL AND CL DOMAINS) CHAIN D (VH AND CH1 DOMAINS) AND CHAIN F (HEL). THE CL C-TERMINAL RESIDUE CYS 214 OF COMPLEX NUMBER 1, THE CL C-TERMINAL RESIDUES LYS 213 AND CYS 214 AND CH1 RESIDUES GLY 130 - ASN 136, THR 195, AND VAL 214 HAVE NO ELECTRON DENSITY AND HAVE BEEN ASSIGNED OCCUPANCIES OF 0.01. IN ADDITION, THE 14 C-TERMINAL RESIDUES OF THE HEL OF COMPLEX NUMBER 1 ARE POORLY RESOLVED. ATOMIC POSITIONS FOR ATOMS OF THESE RESIDUES SHOULD BE CONSIDERED ARBITRARY.
RfactorNum. reflection
Rfree0.282 -
obs0.184 42713
Displacement parametersBiso mean: 27.1 Å2
Refinement stepCycle: LAST / Resolution: 2.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8582 0 0 210 8792
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0410.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0510.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.861
X-RAY DIFFRACTIONp_mcangle_it1.561.5
X-RAY DIFFRACTIONp_scbond_it1.271.5
X-RAY DIFFRACTIONp_scangle_it2.042
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr1670.15
X-RAY DIFFRACTIONp_singtor_nbd0.220.4
X-RAY DIFFRACTIONp_multtor_nbd0.270.4
X-RAY DIFFRACTIONp_xhyhbond_nbd0.230.4
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.43
X-RAY DIFFRACTIONp_staggered_tor23.115
X-RAY DIFFRACTIONp_orthonormal_tor20.120
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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