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Yorodumi- PDB-6sw4: The structure of AraP, an arabinose binding protein from Geobacil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sw4 | ||||||
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Title | The structure of AraP, an arabinose binding protein from Geobacillus stearothermophilus | ||||||
Components | Arabinose binding protein | ||||||
Keywords | SUGAR BINDING PROTEIN / Geobacillus stearothermophilus / binding protein / arabinose / three component sensing system | ||||||
Function / homology | Periplasmic binding protein / Periplasmic binding protein domain / Periplasmic binding protein-like I / Arabinose binding protein Function and homology information | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.845 Å | ||||||
Authors | Lansky, S. / Salama, R. / Lavid, N. / Shoham, Y. / Shoham, G. | ||||||
Citation | Journal: To Be Published Title: The structure of AraP, an arabinose binding protein from Geobacillus stearothermophilus Authors: Lansky, S. / Salama, R. / Lavid, N. / Shoham, Y. / Shoham, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sw4.cif.gz | 127.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sw4.ent.gz | 99.2 KB | Display | PDB format |
PDBx/mmJSON format | 6sw4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sw/6sw4 ftp://data.pdbj.org/pub/pdb/validation_reports/sw/6sw4 | HTTPS FTP |
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-Related structure data
Related structure data | 3g1wS S: Starting model for refinement |
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Similar 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: 37039.055 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: araP / Production host: Escherichia coli (E. coli) / References: UniProt: B3EYL5 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 23% PEG 8K, 0.1 M acetate buffer pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→50 Å / Num. obs: 50563 / % possible obs: 99.6 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.84→1.96 Å / Rmerge(I) obs: 1.357 / Num. unique obs: 7925 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3G1W Resolution: 1.845→43.984 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.69 Å2 / Biso mean: 47.0996 Å2 / Biso min: 17.54 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.845→43.984 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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