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Yorodumi- PDB-1mlc: MONOCLONAL ANTIBODY FAB D44.1 RAISED AGAINST CHICKEN EGG-WHITE LY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mlc | ||||||
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Title | MONOCLONAL ANTIBODY FAB D44.1 RAISED AGAINST CHICKEN EGG-WHITE LYSOZYME COMPLEXED WITH LYSOZYME | ||||||
Components |
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Keywords | COMPLEX (ANTIBODY/ANTIGEN) / COMPLEX (ANTIBODY-ANTIGEN) / COMPLEX (ANTIBODY-ANTIGEN) complex | ||||||
Function / homology | Function and homology information humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding ...humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin mediated immune response / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / B cell differentiation / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / positive regulation of immune response / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / antibacterial humoral response / killing of cells of another organism / defense response to Gram-negative bacterium / 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 | ||||||
Biological species | Mus musculus (house mouse) Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Braden, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mlc.cif.gz | 221.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mlc.ent.gz | 184.6 KB | Display | PDB format |
PDBx/mmJSON format | 1mlc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/1mlc ftp://data.pdbj.org/pub/pdb/validation_reports/ml/1mlc | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Atom site foot note | 1: 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 |
-Components
#1: Antibody | 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 | 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 | 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 / | Compound details | VL 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). | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.39 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 Å |
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Detector | Type: SIEMENS / Detector: AREA DETECTOR |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. 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 |
-Processing
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Refinement | Resolution: 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.
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Displacement parameters | Biso mean: 27.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→7 Å
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Refine LS restraints |
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