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- PDB-2v7h: Crystal structure of an immunogen specific anti-mannopyranoside m... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2v7h | ||||||
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Title | Crystal structure of an immunogen specific anti-mannopyranoside monoclonal antibody Fab fragment | ||||||
![]() | (MONOCLONAL ANTIBODY) x 2 | ||||||
![]() | IMMUNE SYSTEM / MONOCLONAL ANTIBODY / MANNOPYRANOSIDE SPECIFICITY / MOLECULAR MIMICRY | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Krishnan, L. / Sahni, G. / Kaur, K.J. / Salunke, D.M. | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 176 KB | Display | ![]() |
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PDB format | ![]() | 139.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.5 KB | Display | ![]() |
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Full document | ![]() | 535.4 KB | Display | |
Data in XML | ![]() | 42.6 KB | Display | |
Data in CIF | ![]() | 57.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fabS S: Starting model for refinement |
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Similar structure data |
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Links
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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) ![]() ![]() #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) ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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