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- PDB-4inx: Structure of Pheromone-binding protein 1 in complex with (Z,Z)-11... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4inx | ||||||
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Title | Structure of Pheromone-binding protein 1 in complex with (Z,Z)-11,13- hexadecadienol | ||||||
![]() | Pheromone-binding protein 1 | ||||||
![]() | pheromone-binding protein / Amyelois transitella / pheromone / navel orangeworm moth / AtraPBP1 / pH-dependent binding | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | di Luccio, E. / Wilson, D.K. | ||||||
![]() | ![]() Title: Crystallographic Observation of pH-Induced Conformational Changes in the Amyelois transitella Pheromone-Binding Protein AtraPBP1. Authors: di Luccio, E. / Ishida, Y. / Leal, W.S. / Wilson, D.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 41 KB | Display | ![]() |
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PDB format | ![]() | 31.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 15867.321 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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#2: Chemical | ChemComp-1EX / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.31 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Purified AtraPBP1 was crystallized at room temperature by the hanging drop vapor diffusion method. Drops composed of 1ul protein solution (30 mg/ml) and 1ul of the precipitant solution were ...Details: Purified AtraPBP1 was crystallized at room temperature by the hanging drop vapor diffusion method. Drops composed of 1ul protein solution (30 mg/ml) and 1ul of the precipitant solution were suspended over a reservoir containing the precipitant solution (1.6 M sodium citrate pH 6.5). Crystals used in data collection were transferred into Paratone-N oil and flash-cooled in a stream of liquid nitrogen at 110 K, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 12, 2006 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 2.8 % / Av σ(I) over netI: 28.42 / Number: 41040 / Rmerge(I) obs: 0.04 / Χ2: 1.28 / D res high: 1.85 Å / D res low: 50 Å / Num. obs: 14800 / % possible obs: 98.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.85→50 Å / Num. all: 15052 / Num. obs: 14800 / % possible obs: 98.3 % / Observed criterion σ(I): 28.4 / Redundancy: 2.8 % / Rmerge(I) obs: 0.04 / Χ2: 1.276 / Net I/σ(I): 16.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 44.7 Å2 / Biso mean: 13.0968 Å2 / Biso min: 2.82 Å2
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Refinement step | Cycle: LAST / Resolution: 1.853→34.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.853→1.901 Å / Total num. of bins used: 20
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