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Yorodumi- PDB-1vfb: BOUND WATER MOLECULES AND CONFORMATIONAL STABILIZATION HELP MEDIA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vfb | ||||||
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Title | BOUND WATER MOLECULES AND CONFORMATIONAL STABILIZATION HELP MEDIATE AN ANTIGEN-ANTIBODY ASSOCIATION | ||||||
Components |
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Keywords | IMMUNOGLOBULIN/HYDROLASE(O-GLYCOSYL) / IMMUNOGLOBULIN-HYDROLASE(O-GLYCOSYL) complex | ||||||
Function / homology | Function and homology information immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism ...immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / adaptive immune response / defense response to Gram-positive bacterium / defense response to bacterium / immune response / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Bhat, T.N. / Poljak, R.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1994 Title: Bound water molecules and conformational stabilization help mediate an antigen-antibody association. Authors: Bhat, T.N. / Bentley, G.A. / Boulot, G. / Greene, M.I. / Tello, D. / Dall'Acqua, W. / Souchon, H. / Schwarz, F.P. / Mariuzza, R.A. / Poljak, R.J. #1: Journal: Nature / Year: 1990 Title: Small Rearrangements in Structures of Fv and Fab Fragments of an Antibody D1.3 On Antigen Binding Authors: Bhat, T.N. / Bentley, G.A. / Fischmann, T.O. / Boulot, G. / Poljak, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vfb.cif.gz | 89.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vfb.ent.gz | 73 KB | Display | PDB format |
PDBx/mmJSON format | 1vfb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/1vfb ftp://data.pdbj.org/pub/pdb/validation_reports/vf/1vfb | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO A 8 / 2: CIS PROLINE - PRO A 95 |
-Components
#1: Antibody | Mass: 11700.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Organ: EGG / Production host: Escherichia coli (E. coli) / References: GenBank: 545862, UniProt: P01635*PLUS |
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#2: Antibody | Mass: 12857.275 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Organ: EGG / Production host: Escherichia coli (E. coli) / References: GenBank: 896294, UniProt: P01820*PLUS |
#3: Protein | Mass: 14331.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P00698 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.9 % | |||||||||||||||
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Crystal grow | *PLUS pH: 5.85 / Method: vapor diffusion | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.8 Å / Num. obs: 29495 / % possible obs: 90 % / Num. measured all: 53556 / Rmerge(I) obs: 0.063 |
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-Processing
Software |
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Refinement | Rfactor Rwork: 0.185 / Rfactor obs: 0.185 / Highest resolution: 1.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 7 Å / Num. reflection obs: 28534 / σ(F): 2 / Rfactor obs: 0.185 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.7 |