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Open data
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Basic information
Entry | Database: PDB / ID: 3gaq | ||||||
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Title | Female-specific Histamine-Binding Protein, D24R Mutant | ||||||
![]() | Female-specific histamine-binding protein 2 | ||||||
![]() | IMMUNE SYSTEM / Lipocalin / Beta barrel | ||||||
Function / homology | ![]() amine binding / symbiont-mediated perturbation of host defenses / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dennis, C.A. / Homans, S.W. | ||||||
![]() | ![]() Title: Entropic contributions to binding in a 'Hydrophilic' Ligand-Protein Interaction Authors: Syme, N.R. / Dennis, C.A. / Bronowska, A. / Paesen, G. / Homans, S.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.3 KB | Display | ![]() |
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PDB format | ![]() | 63.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.6 KB | Display | ![]() |
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Full document | ![]() | 440.1 KB | Display | |
Data in XML | ![]() | 16.8 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3g7xC ![]() 1qftS C: citing same article ( 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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Components
#1: Protein | Mass: 19597.230 Da / Num. of mol.: 2 / Mutation: D24R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pET23a / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.82 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: Protein at 10 mg/ml mixed in a 1:1 ratio with reservoir containing: 2.6 M Ammonium Sulphate, 0.1 M Bicine, pH 8.2, and 10 % isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 8, 2008 / Details: mirrors |
Radiation | Monochromator: confocal max-flux optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→12 Å / Num. obs: 18800 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 34.75 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.1 / Num. unique all: 2735 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1QFT Resolution: 2.25→11.96 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.879 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.997 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.371 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.03 Å2 / Biso mean: 46.094 Å2 / Biso min: 28.37 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→11.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.306 Å / Total num. of bins used: 20
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