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Yorodumi- PDB-4inx: Structure of Pheromone-binding protein 1 in complex with (Z,Z)-11... -
+Open data
-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 | ||||||
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: 1.853 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 | 4inx.cif.gz | 41 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4inx.ent.gz | 31.4 KB | Display | PDB format |
PDBx/mmJSON format | 4inx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/4inx ftp://data.pdbj.org/pub/pdb/validation_reports/in/4inx | HTTPS FTP |
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-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-1EX / ( |
#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: 2.82 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: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.853→34.1 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 2.427 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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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