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- PDB-5nbw: Crystal structure of the Fab fragment 22F12 in complex with 3-hyd... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nbw | ||||||
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Title | Crystal structure of the Fab fragment 22F12 in complex with 3-hydroxybenzo[a]pyrene | ||||||
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![]() | IMMUNE SYSTEM / antibody / benzo[a]pyrene / Fab fragment / hapten | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / benzo[a]pyren-3-ol![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Skerra, A. / Eichinger, A. | ||||||
![]() | ![]() Title: Tight Molecular Recognition of Benzo[a]pyrene by a High-Affinity Antibody. Authors: Eichinger, A. / Neumaier, I. / Pschenitza, M. / Niessner, R. / Knopp, D. / Skerra, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 339.2 KB | Display | ![]() |
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PDB format | ![]() | 277.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4m1gS 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 domain:
NCS domain segments: Component-ID: _ / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: _
NCS ensembles :
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Components
#1: Antibody | Mass: 23950.447 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Antibody | Mass: 24085.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 2.2 M Na-malonate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2014 / Details: mirrors |
Radiation | Monochromator: Si 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→61.1 Å / Num. obs: 35232 / % possible obs: 99.8 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 5049 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4M1G Resolution: 2.4→61.1 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / SU B: 17.963 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.482 / ESU R Free: 0.253 / 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: 36.331 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→61.1 Å
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Refine LS restraints |
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