+Open data
-Basic information
Entry | Database: PDB / ID: 1bvk | ||||||
---|---|---|---|---|---|---|---|
Title | HUMANIZED ANTI-LYSOZYME FV COMPLEXED WITH LYSOZYME | ||||||
Components |
| ||||||
Keywords | COMPLEX (HUMANIZED ANTIBODY/HYDROLASE) / HUMANIZED ANTIBODY / ANTIBODY COMPLEX / FV / ANTI-LYSOZYME / COMPLEX (HUMANIZED ANTIBODY-HYDROLASE) / COMPLEX (HUMANIZED ANTIBODY-HYDROLASE) complex | ||||||
Function / homology | Function and homology information 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 / defense response to Gram-positive bacterium / defense response to bacterium ...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 / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Holmes, M.A. / Buss, T.N. / Foote, J. | ||||||
Citation | Journal: J.Exp.Med. / Year: 1998 Title: Conformational correction mechanisms aiding antigen recognition by a humanized antibody. Authors: Holmes, M.A. / Buss, T.N. / Foote, J. #1: Journal: J.Immunol. / Year: 1997 Title: Structural Consequences of Humanizing an Antibody Authors: Holmes, M.A. / Foote, J. #2: Journal: J.Mol.Biol. / Year: 1992 Title: Antibody Framework Residues Affecting the Conformation of the Hypervariable Loops Authors: Foote, J. / Winter, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1bvk.cif.gz | 139.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1bvk.ent.gz | 114.8 KB | Display | PDB format |
PDBx/mmJSON format | 1bvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/1bvk ftp://data.pdbj.org/pub/pdb/validation_reports/bv/1bvk | HTTPS FTP |
---|
-Related structure data
Related structure data | 1vfbS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.999987, 0.002639, 0.004298), Vector: |
-Components
#1: Antibody | Mass: 11962.320 Da / Num. of mol.: 2 / Fragment: FV Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): 25F2 / References: PIR: S21680 #2: Antibody | Mass: 12872.358 Da / Num. of mol.: 2 / Fragment: FV Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): 25F2 / References: PIR: S21681 #3: Protein | Mass: 14331.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Description: EGG WHITE / Production host: Escherichia coli (E. coli) / Strain (production host): 25F2 / References: UniProt: P00698, lysozyme |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.9 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 277 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
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 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.82 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.326 |