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Yorodumi- PDB-6eq0: Structure of the periplasmic binding protein (PBP) MelB (atu4661)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6eq0 | ||||||
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Title | Structure of the periplasmic binding protein (PBP) MelB (atu4661) in complex with galactose from agrobacterium tumefacien C58 | ||||||
Components | Periplasmic alpha-galactoside-binding protein | ||||||
Keywords | TRANSPORT PROTEIN / Protein transport associated to ABC transporter | ||||||
Function / homology | Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / periplasmic space / alpha-D-galactopyranose / DI(HYDROXYETHYL)ETHER / Periplasmic alpha-galactoside-binding protein Function and homology information | ||||||
Biological species | Rhizobium radiobacter (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Vigouroux, A. / Morera, S. | ||||||
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 | 6eq0.cif.gz | 549.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eq0.ent.gz | 455.3 KB | Display | PDB format |
PDBx/mmJSON format | 6eq0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6eq0_validation.pdf.gz | 491.6 KB | Display | wwPDB validaton report |
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Full document | 6eq0_full_validation.pdf.gz | 506.7 KB | Display | |
Data in XML | 6eq0_validation.xml.gz | 51.1 KB | Display | |
Data in CIF | 6eq0_validation.cif.gz | 71 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/6eq0 ftp://data.pdbj.org/pub/pdb/validation_reports/eq/6eq0 | HTTPS FTP |
-Related structure data
Related structure data | 6epyC 6epzSC 6eq1C 6eq8C 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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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 76359.602 Da / Num. of mol.: 2 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: Sugar | |
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-Non-polymers , 5 types, 309 molecules
#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-CA / #7: 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: 2.23 Å3/Da / Density % sol: 44.86 % |
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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 2 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 6, 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: 2.45→50 Å / Num. obs: 49700 / % possible obs: 99.2 % / Redundancy: 6.3 % / Biso Wilson estimate: 63.81 Å2 / CC1/2: 0.991 / Rsym value: 0.182 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.45→2.59 Å / Mean I/σ(I) obs: 1.6 / CC1/2: 0.512 / Rsym value: 1 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EPZ Resolution: 2.45→46.51 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.891 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.665 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.598 / SU Rfree Blow DPI: 0.27 / SU Rfree Cruickshank DPI: 0.278
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Displacement parameters | Biso mean: 65.47 Å2
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Refine analyze | Luzzati coordinate error obs: 0.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.45→46.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.51 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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