+Open data
-Basic information
Entry | Database: PDB / ID: 1mpa | |||||||||
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Title | BACTERICIDAL ANTIBODY AGAINST NEISSERIA MENINGITIDIS | |||||||||
Components |
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Keywords | COMPLEX (IMMUNOGLOBULIN/PEPTIDE) / MURINE IMMUNOGLOBULIN IGG2A KAPPA / BACTERICIDAL ANTIBODY / EPITOPE P1.16 OF PORA FROM NEISSERIA MENINGITIDIS / COMPLEX (IMMUNOGLOBULIN-PEPTIDE) / COMPLEX (IMMUNOGLOBULIN-PEPTIDE) complex | |||||||||
Function / homology | Function and homology information immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / immune response / extracellular space / extracellular exosome / metal ion binding Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Van Den Elsen, J.M.H. / Herron, J.N. / Kroon, J. / Gros, P. | |||||||||
Citation | Journal: Proteins / Year: 1997 Title: Bactericidal antibody recognition of a PorA epitope of Neisseria meningitidis: crystal structure of a Fab fragment in complex with a fluorescein-conjugated peptide. Authors: van den Elsen, J.M. / Herron, J.N. / Hoogerhout, P. / Poolman, J.T. / Boel, E. / Logtenberg, T. / Wilting, J. / Crommelin, D.J. / Kroon, J. / Gros, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mpa.cif.gz | 119.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mpa.ent.gz | 90.7 KB | Display | PDB format |
PDBx/mmJSON format | 1mpa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mpa_validation.pdf.gz | 453.7 KB | Display | wwPDB validaton report |
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Full document | 1mpa_full_validation.pdf.gz | 468.7 KB | Display | |
Data in XML | 1mpa_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 1mpa_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/1mpa ftp://data.pdbj.org/pub/pdb/validation_reports/mp/1mpa | HTTPS FTP |
-Related structure data
Related structure data | 2mpaC 2hfl S: Starting model for refinement C: citing same article (ref.) |
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Similar 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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-Components
#1: Antibody | Mass: 24122.861 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell: B-LYMPHOCYTE HYBRIDOMA Cell line (production host): MN12H2 MURINE-MURINE HYBRIDOMA CELL LINE Production host: Mus musculus (house mouse) / References: PIR: PC4203, UniProt: A2NHM3*PLUS |
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#2: Antibody | Mass: 24415.350 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell: B-LYMPHOCYTE HYBRIDOMA Cell line (production host): MN12H2 MURINE-MURINE HYBRIDOMA CELL LINE Production host: Mus musculus (house mouse) / References: PIR: S38950, UniProt: Q569X1*PLUS |
#3: Protein/peptide | Mass: 1453.509 Da / Num. of mol.: 1 Fragment: APEX OF EXTRACELLULAR LOOP 4 (VR2) OF PORA, RESIDUES 180 - 187 Source method: isolated from a genetically manipulated source |
#4: Chemical | ChemComp-CD / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % |
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Crystal grow | pH: 4.6 Details: THE MN12H2 FAB PEPTIDE COMPLEX WAS CRYSTALLIZED FROM 15% W/V PEG 20000, 100 MM SODIUM ACETATE, PH 4.6, 20 MM CDCL. |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: MAC Science DIP-2020 / Detector: IMAGE PLATE / Date: Mar 1, 1995 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 15404 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 37.1 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.357 / % possible all: 96.5 |
Reflection | *PLUS Num. measured all: 94382 |
Reflection shell | *PLUS % possible obs: 96.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HFL 2hfl Resolution: 2.6→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 27.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.35 Å / Luzzati d res low obs: 8 Å / Luzzati sigma a obs: 0.46 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.71 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.63 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.34 |