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Yorodumi- PDB-1m7i: CRYSTAL STRUCTURE OF A MONOCLONAL FAB SPECIFIC FOR SHIGELLA FLEXN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m7i | |||||||||
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Title | CRYSTAL STRUCTURE OF A MONOCLONAL FAB SPECIFIC FOR SHIGELLA FLEXNERI Y LIPOPOLYSACCHARIDE COMPLEXED WITH A PENTASACCHARIDE | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Fab-carbohydrate interactions / Shigella O-antigen / and anti-carbohydrate antibody | |||||||||
Function / homology | Function and homology information immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Vyas, N.K. / Vyas, M.N. / Chervenak, M.C. / Johnson, M.A. / Pinto, B.M. / Bundle, D.R. / Quiocho, F.A. | |||||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Molecular Recognition of Oligosaccharide Epitopes by a Monoclonal Fab Specific for Shigella flexneri Y Lipopolysaccharide: X-ray Structures and Thermodynamics Authors: Vyas, N.K. / Vyas, M.N. / Chervenak, M.C. / Johnson, M.A. / Pinto, B.M. / Bundle, D.R. / Quiocho, F.A. #1: Journal: J.Mol.Biol. / Year: 1993 Title: Preliminary Crystallographic Analysis of a Fab Specific for the O-antigen of Shigella flexneri Cell Surface Lipoplysacharide with and and without Bound Saccharides Authors: Vyas, N.K. / Vyas, M.N. / Chervenak, M.C. / Johnson, M.A. / Pinto, B.M. / Bundle, D.R. / Quiocho, F.A. | |||||||||
History |
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Remark 999 | SEQUENCE At the time of processing, this sequence of chain A and chain B have not yet been ...SEQUENCE At the time of processing, this sequence of chain A and chain B have not yet been deposited in a sequence database. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m7i.cif.gz | 97.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m7i.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 1m7i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m7/1m7i ftp://data.pdbj.org/pub/pdb/validation_reports/m7/1m7i | HTTPS FTP |
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-Related structure data
Related structure data | 1m71C 1m7dC 1mcpS 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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Unit cell |
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-Components
#1: Antibody | Mass: 23717.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/C / Cell: Plasmacytoma cell / Cell line: SYA/J6 hybridoma / Organ: Spleen / Production host: Escherichia coli (E. coli) / References: UniProt: A2NHM3*PLUS |
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#2: Antibody | Mass: 23547.361 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/C / Cell: Plasmacytoma cell / Cell line: SYA/J6 hybridoma / Organ: Spleen / Production host: Escherichia coli (E. coli) / References: UniProt: P01801*PLUS |
#3: Polysaccharide | alpha-L-rhamnopyranose-(1-2)-alpha-L-rhamnopyranose-(1-3)-alpha-L-rhamnopyranose-(1-3)-2-acetamido- ...alpha-L-rhamnopyranose-(1-2)-alpha-L-rhamnopyranose-(1-3)-alpha-L-rhamnopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-methyl 6-deoxy-alpha-L-rhamnopyranoside Source method: isolated from a genetically manipulated source |
#4: 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: 2.67 Å3/Da / Density % sol: 53.92 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6.5 Details: MPD, potassium phosphate, pH 6.5, VAPOR DIFFUSION, temperature 277K |
Crystal grow | *PLUS Details: Vyas, M.N., (1993) J. Mol. Biol., 231, 133. |
-Data collection
Diffraction | Mean temperature: 281 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Jun 2, 1990 / Details: hoton Factory BL6A2 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 14764 / Num. obs: 14375 / % possible obs: 79.6 % / Observed criterion σ(I): 1.5 / Redundancy: 6.5 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.075 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.5→2.66 Å / Num. unique all: 737 / % possible all: 55.2 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. measured all: 108148 |
Reflection shell | *PLUS % possible obs: 55.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MCP Resolution: 2.5→20 Å / Rfactor Rfree error: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1.5 / Stereochemistry target values: Engh & Huber Details: Author states residues 127-135 of chain B is part of a disordered segment.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.142 Å2 / ksol: 0.302051 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.207 | |||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.411 |