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Yorodumi- PDB-6epy: Structure of the PBP MelB (Atu4661) in complex with raffinose fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6epy | |||||||||
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Title | Structure of the PBP MelB (Atu4661) in complex with raffinose from A.fabrum C58 | |||||||||
Components | Periplasmic alpha-galactoside-binding protein | |||||||||
Keywords | TRANSPORT PROTEIN / Periplasmic binding protein | |||||||||
Function / homology | Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / periplasmic space / raffinose / Periplasmic alpha-galactoside-binding protein Function and homology information | |||||||||
Biological species | Rhizobium radiobacter (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å | |||||||||
Authors | Morera, S. / Vigouroux, A. | |||||||||
Funding support | France, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: The plant defense signal galactinol is specifically used as a nutrient by the bacterial pathogenAgrobacterium fabrum. Authors: Meyer, T. / Vigouroux, A. / Aumont-Nicaise, M. / Comte, G. / Vial, L. / Lavire, C. / Morera, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6epy.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6epy.ent.gz | 901.5 KB | Display | PDB format |
PDBx/mmJSON format | 6epy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6epy_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 6epy_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6epy_validation.xml.gz | 102.9 KB | Display | |
Data in CIF | 6epy_validation.cif.gz | 148.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/6epy ftp://data.pdbj.org/pub/pdb/validation_reports/ep/6epy | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 77063.047 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium radiobacter (bacteria) / Gene: SY94_4618 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A083ZM57 #2: Polysaccharide | alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose-(1-2)-beta-D-fructofuranose / raffinose #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-CA / #5: 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: 25% PEG 4000, 0.6 M NaCl, 0.2 M CaCl2 and 0.1 M Mes pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2015 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→45.14 Å / Num. obs: 333472 / % possible obs: 98.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 39.76 Å2 / CC1/2: 0.998 / Rsym value: 0.07 / Net I/σ(I): 10.84 |
Reflection shell | Resolution: 2.04→2.17 Å / CC1/2: 0.801 / Rsym value: 0.528 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.04→45.14 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.185 / SU Rfree Blow DPI: 0.146 / SU Rfree Cruickshank DPI: 0.148
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Displacement parameters | Biso mean: 44.74 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.04→45.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.04→2.09 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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