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Yorodumi- PDB-2v7h: Crystal structure of an immunogen specific anti-mannopyranoside m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v7h | ||||||
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Title | Crystal structure of an immunogen specific anti-mannopyranoside monoclonal antibody Fab fragment | ||||||
Components | (MONOCLONAL ANTIBODY) x 2 | ||||||
Keywords | IMMUNE SYSTEM / MONOCLONAL ANTIBODY / MANNOPYRANOSIDE SPECIFICITY / MOLECULAR MIMICRY | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Krishnan, L. / Sahni, G. / Kaur, K.J. / Salunke, D.M. | ||||||
Citation | Journal: Biophys.J. / Year: 2008 Title: Role of Antibody Paratope Conformational Flexibility in the Manifestation of Molecular Mimicry. Authors: Krishnan, L. / Sahni, G. / Kaur, K.J. / Salunke, D.M. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v7h.cif.gz | 176 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v7h.ent.gz | 139.1 KB | Display | PDB format |
PDBx/mmJSON format | 2v7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v7h_validation.pdf.gz | 463.5 KB | Display | wwPDB validaton report |
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Full document | 2v7h_full_validation.pdf.gz | 535.4 KB | Display | |
Data in XML | 2v7h_validation.xml.gz | 42.6 KB | Display | |
Data in CIF | 2v7h_validation.cif.gz | 57.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/2v7h ftp://data.pdbj.org/pub/pdb/validation_reports/v7/2v7h | HTTPS FTP |
-Related structure data
Related structure data | 6fabS S: Starting model for refinement |
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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: 23632.947 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT LIGHT CHAIN / Source method: isolated from a natural source Details: MONOCLONAL ANTIBODY AGAINST ALPHA-D-MANNOPYRANOSIDE Source: (natural) MUS MUSCULUS (house mouse) / Cell: B-LYMPHOCYTE / Cell line: 1H7 MURINE HYBRIDOMA / Strain: BALB/C #2: Antibody | Mass: 23789.480 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT HEAVY CHAIN / Source method: isolated from a natural source Details: MONOCLONAL ANTIBODY AGAINST ALPHA-D-MANNOPYRANOSIDE Source: (natural) MUS MUSCULUS (house mouse) / Cell: B-LYMPHOCYTE / Cell line: 1H7 MURINE HYBRIDOMA / Strain: BALB/C #3: Water | ChemComp-HOH / | |
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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: 2.2 Å3/Da / Density % sol: 43.5 % / Description: NONE |
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Crystal grow | pH: 7.4 / Details: 50MM TRISCL, PH 7.4 WITH 20% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 20, 2003 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 19865 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 3.25 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.23 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.2 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 6FAB Resolution: 2.8→17.46 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF Details: DISORDERED REGIONS IN THE PROTEIN HAVE NOT BEEN MODELED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.0601 Å2 / ksol: 0.290378 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.68 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→17.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.9 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
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Xplor file |
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