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Yorodumi- PDB-4inw: Structure of Pheromone-binding protein 1 in complex with (11Z,13Z... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4inw | ||||||
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Title | Structure of Pheromone-binding protein 1 in complex with (11Z,13Z)-hexadecadienal | ||||||
Components | Pheromone-binding protein 1 | ||||||
Keywords | pheromone-binding protein / Amyelois transitella / pheromone / navel orangeworm moth / AtraPBP1 / pH-dependent binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Amyelois transitella (butterflies/moths) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.14 Å | ||||||
Authors | di Luccio, E. / Wilson, D.K. | ||||||
Citation | Journal: Plos One / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4inw.cif.gz | 72.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4inw.ent.gz | 58.4 KB | Display | PDB format |
PDBx/mmJSON format | 4inw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4inw_validation.pdf.gz | 439.5 KB | Display | wwPDB validaton report |
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Full document | 4inw_full_validation.pdf.gz | 443 KB | Display | |
Data in XML | 4inw_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 4inw_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/4inw ftp://data.pdbj.org/pub/pdb/validation_reports/in/4inw | HTTPS FTP |
-Related structure data
-Links
-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.) Amyelois transitella (butterflies/moths) Production host: Escherichia coli (E. coli) / References: UniProt: D0E9M1 |
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#2: Chemical | ChemComp-1EY / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.08 % |
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Crystal grow | Temperature: 295 K / 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: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.1 |
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: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.14→28.72 Å / % possible obs: 97.2 % / Observed criterion σ(I): 29.3 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.14→28.72 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 1.384 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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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 mean: 17.23 Å2
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Refinement step | Cycle: LAST / Resolution: 1.14→28.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.14→1.17 Å / Total num. of bins used: 20
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