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Yorodumi- PDB-6rkx: The crystal structure of AbnE, an arabino-oligosaccharide binding... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rkx | |||||||||
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Title | The crystal structure of AbnE, an arabino-oligosaccharide binding protein, in complex with arabinopentaose | |||||||||
Components | Arabino-oligosaccharids-binding protein | |||||||||
Keywords | SUGAR BINDING PROTEIN / Geobacillus stearothermophilus / ABC transporter / arabino-oligosaccharide / arabinopentaose | |||||||||
Function / homology | Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / Arabino-oligosaccharids-binding protein Function and homology information | |||||||||
Biological species | Geobacillus stearothermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.094 Å | |||||||||
Authors | Lansky, S. / Salama, R. / Shoham, Y. / Shoham, G. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2020 Title: Carbohydrate-Binding Capability and Functional Conformational Changes of AbnE, an Arabino-oligosaccharide Binding Protein. Authors: Lansky, S. / Salama, R. / Shulami, S. / Lavid, N. / Sen, S. / Schapiro, I. / 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 | 6rkx.cif.gz | 108 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rkx.ent.gz | 79.6 KB | Display | PDB format |
PDBx/mmJSON format | 6rkx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rkx_validation.pdf.gz | 723.6 KB | Display | wwPDB validaton report |
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Full document | 6rkx_full_validation.pdf.gz | 726.9 KB | Display | |
Data in XML | 6rkx_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 6rkx_validation.cif.gz | 30.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/6rkx ftp://data.pdbj.org/pub/pdb/validation_reports/rk/6rkx | HTTPS FTP |
-Related structure data
Related structure data | 6rjyC 6rkhSC 6rkjC 6rklC 6rl1C 6rl2C C: citing same article (ref.) 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: 48689.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: abnE / Production host: Escherichia coli (E. coli) / References: UniProt: B3EYM9 | ||||
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#2: Polysaccharide | alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L- ...alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose Source method: isolated from a genetically manipulated source | ||||
#3: Chemical | #4: Chemical | ChemComp-CA / | #5: 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: 2.35 Å3/Da / Density % sol: 47.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 22% PEG 4K, 0.1M Tris/HCl buffer, pH 9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.094→35 Å / Num. obs: 26581 / % possible obs: 98.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.094→2.19 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1262 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6RKH Resolution: 2.094→30.96 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.12
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.094→30.96 Å
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Refine LS restraints |
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LS refinement shell |
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