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Open data
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Basic information
Entry | Database: PDB / ID: 1lp1 | ||||||
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Title | Protein Z in complex with an in vitro selected affibody | ||||||
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![]() | IMMUNE SYSTEM / in vitro evolved / protein-protein complex / three-helix bundle / affibody | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hogbom, M. / Eklund, M. / Nygren, P.A. / Nordlund, P. | ||||||
![]() | ![]() Title: Structural basis for recognition by an in vitro evolved affibody. Authors: Hogbom, M. / Eklund, M. / Nygren, P.A. / Nordlund, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 39.8 KB | Display | ![]() |
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PDB format | ![]() | 27.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.3 KB | Display | ![]() |
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Full document | ![]() | 450.8 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 12.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1deeS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 6447.263 Da / Num. of mol.: 1 / Fragment: In vitro selected binding protein Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Antibody | Mass: 6648.316 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-58 / Mutation: A1V, G29A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.45 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: MgSO4, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 1, 2001 |
Radiation | Monochromator: asymmetrically cut Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.098 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 6899 / Num. obs: 6899 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 51.3 Å2 / Rmerge(I) obs: 0.05 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.296 / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 6847 / % possible obs: 99.7 % / Num. measured all: 57198 / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 99.8 % / Rmerge(I) obs: 0.29 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Polyserine model of PDB entry 1DEE, chain G Resolution: 2.3→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.255 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.17 |