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Yorodumi- PDB-1mam: CRYSTAL STRUCTURE TO 2.45 A RESOLUTION OF A MONOCLONAL FAB SPECIF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mam | ||||||
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Title | CRYSTAL STRUCTURE TO 2.45 A RESOLUTION OF A MONOCLONAL FAB SPECIFIC FOR THE BRUCELLA A CELL WALL POLYSACCHARIDE ANTIGEN | ||||||
Components |
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Keywords | IMMUNOGLOBULIN | ||||||
Function / homology | Function and homology information Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / 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 / positive regulation of immune response / antibacterial humoral response / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.45 Å | ||||||
Authors | Rose, D.R. | ||||||
Citation | Journal: Protein Sci. / Year: 1993 Title: Crystal structure to 2.45 A resolution of a monoclonal Fab specific for the Brucella A cell wall polysaccharide antigen. Authors: Rose, D.R. / Przybylska, M. / To, R.J. / Kayden, C.S. / Oomen, R.P. / Vorberg, E. / Young, N.M. / Bundle, D.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mam.cif.gz | 90.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mam.ent.gz | 72.9 KB | Display | PDB format |
PDBx/mmJSON format | 1mam.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/1mam ftp://data.pdbj.org/pub/pdb/validation_reports/ma/1mam | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: THR L 43 - VAL L 44 OMEGA ANGLE = 34.342 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: CIS PROLINE - PRO L 95 / 3: CIS PROLINE - PRO L 141 4: SER H 79 - ILE H 80 OMEGA ANGLE = 139.405 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 5: CIS PROLINE - PRO H 105 6: GLY H 135 - ASP H 136 OMEGA ANGLE = 245.392 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 7: SER H 141 - VAL H 142 OMEGA ANGLE = 140.185 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 8: CIS PROLINE - PRO H 153 9: SER H 155 - VAL H 156 OMEGA ANGLE = 122.634 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 10: SER H 166 - SER H 167 OMEGA ANGLE = 263.733 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 11: CIS PROLINE - PRO H 195 |
-Components
#1: Antibody | Mass: 23772.162 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) |
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#2: Antibody | Mass: 23156.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P01867 |
Sequence details | THE RESIDUE NUMBERING IS SEQUENTIAL WITHIN EACH CHAIN. THE SEQUENTIAL NUMBERING OF THE LIGHT CHAIN ...THE RESIDUE NUMBERING IS SEQUENTIAL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.63 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.42 Å / Num. all: 17763 / Num. obs: 15355 / Num. measured all: 37288 / Rmerge(I) obs: 0.0517 |
-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.215 / Highest resolution: 2.45 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.45 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.45 Å / Num. reflection obs: 3296 / Rfactor obs: 0.215 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.45 Å / Lowest resolution: 2.6 Å / Num. reflection obs: 1750 / Rfactor obs: 0.27 |