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Open data
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Basic information
Entry | Database: PDB / ID: 1bvk | ||||||
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Title | HUMANIZED ANTI-LYSOZYME FV COMPLEXED WITH LYSOZYME | ||||||
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![]() | COMPLEX (HUMANIZED ANTIBODY/HYDROLASE) / HUMANIZED ANTIBODY / ANTIBODY COMPLEX / FV / ANTI-LYSOZYME / COMPLEX (HUMANIZED ANTIBODY-HYDROLASE) / COMPLEX (HUMANIZED ANTIBODY-HYDROLASE) complex | ||||||
Function / homology | ![]() Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Holmes, M.A. / Buss, T.N. / Foote, J. | ||||||
![]() | ![]() Title: Conformational correction mechanisms aiding antigen recognition by a humanized antibody. Authors: Holmes, M.A. / Buss, T.N. / Foote, J. #1: ![]() Title: Structural Consequences of Humanizing an Antibody Authors: Holmes, M.A. / Foote, J. #2: ![]() Title: Antibody Framework Residues Affecting the Conformation of the Hypervariable Loops Authors: Foote, J. / Winter, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139.2 KB | Display | ![]() |
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PDB format | ![]() | 114.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 400.8 KB | Display | ![]() |
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Full document | ![]() | 431.3 KB | Display | |
Data in XML | ![]() | 18.5 KB | Display | |
Data in CIF | ![]() | 27.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1vfbS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.999987, 0.002639, 0.004298), Vector: |
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Components
#1: Antibody | Mass: 11962.320 Da / Num. of mol.: 2 / Fragment: FV Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 12872.358 Da / Num. of mol.: 2 / Fragment: FV Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 14331.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.9 % | ||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: R-AXIS IIC |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 22379 / % possible obs: 93.2 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 44.1 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.7→2.75 Å / Rmerge(I) obs: 0.452 / Rsym value: 0.452 / % possible all: 73.5 |
Reflection | *PLUS Num. measured all: 120820 |
Reflection shell | *PLUS % possible obs: 73.5 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: HULYS STRUCTURE, AND LYSOZYME FROM PDB ENTRY 1VFB Resolution: 2.7→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: A FEW CYCLES OF TNT REFINEMENT WERE INTERSPERSED WITH THE X-PLOR CYCLES.
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Displacement parameters | Biso mean: 31.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.82 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.326 |