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Open data
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Basic information
Entry | Database: PDB / ID: 5xqw | ||||||
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Title | Catalytic antibody 7B9 | ||||||
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![]() | IMMUNE SYSTEM / catalytic antibody / hydrolytic enzyme / Fab / transition-state analogue | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ethyl-[(4-nitrophenyl)methoxy]phosphinic acid![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ito, N. / Fujii, I. / Tsumuraya, T. | ||||||
![]() | ![]() Title: Structural basis of the broad substrate tolerance of the antibody 7B9-catalyzed hydrolysis of p-nitrobenzyl esters. Authors: Miyamoto, N. / Yoshimura, M. / Okubo, Y. / Suzuki-Nagata, K. / Tsumuraya, T. / Ito, N. / Fujii, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.8 KB | Display | ![]() |
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PDB format | ![]() | 71.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1kb5S 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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Unit cell |
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Components
#1: Antibody | Mass: 23231.611 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 23315.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-8EU / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100mM Tris HCl, 15%(w/v) PEG 1000, 5% 2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Apr 25, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 19632 / % possible obs: 98.8 % / Redundancy: 2.6 % / Rsym value: 0.04 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.324 / % possible all: 95.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KB5 Resolution: 2.2→14.97 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.995 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.364 / ESU R Free: 0.257 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.25 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→14.97 Å
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Refine LS restraints |
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