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Yorodumi- PDB-6j9w: Crystal structure of ABC transporter alpha-glycoside-binding prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6j9w | |||||||||
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Title | Crystal structure of ABC transporter alpha-glycoside-binding protein in complex with trehalose | |||||||||
Components | ABC transporter, periplasmic substrate-binding protein | |||||||||
Keywords | SUGAR BINDING PROTEIN / Carbohydrate-binding site / alpha-glycoside-binding protein / Ligand selection / Multi-substrate transporter / Sugar replacement / Venus Fly-trap mechanism | |||||||||
Function / homology | Function and homology information : / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | |||||||||
Biological species | Thermus thermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | |||||||||
Authors | Kanaujia, S.P. / Chandravanshi, M. / Gogoi, P. | |||||||||
Funding support | India, 1items
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Citation | Journal: Febs J. / Year: 2020 Title: Structural and thermodynamic correlation illuminates the selective transport mechanism of disaccharide alpha-glycosides through ABC transporter. Authors: Chandravanshi, M. / Gogoi, P. / Kanaujia, S.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j9w.cif.gz | 111.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j9w.ent.gz | 81.2 KB | Display | PDB format |
PDBx/mmJSON format | 6j9w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6j9w_validation.pdf.gz | 885.7 KB | Display | wwPDB validaton report |
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Full document | 6j9w_full_validation.pdf.gz | 886.9 KB | Display | |
Data in XML | 6j9w_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 6j9w_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/6j9w ftp://data.pdbj.org/pub/pdb/validation_reports/j9/6j9w | HTTPS FTP |
-Related structure data
Related structure data | 6j9yC 6jadC 6jagC 6jahC 6jaiC 6jalC 6jamC 6janC 6jaoC 6japC 6jaqC 6jarC 6jazC 6jb0C 6jb4C 6jbaC 6jbbC 6jbeC 1eu8S S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 46168.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA0356 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q5SLD7 |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose |
#3: Chemical | ChemComp-CIT / |
#4: Chemical | ChemComp-EDO / |
#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: 2.88 Å3/Da / Density % sol: 57.36 % / Description: Tetragonal |
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 6.4 Details: 0.04 M Citric Acid, 0.06 M Bis-Tris Propane, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 22, 2017 / Details: VariMax HF |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→73.37 Å / Num. obs: 50048 / % possible obs: 99.8 % / Redundancy: 12.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.037 / Rrim(I) all: 0.095 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.8→9 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 2860 / CC1/2: 0.954 / Rpim(I) all: 0.185 / Rrim(I) all: 0.473 / % possible all: 98.9 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EU8 Resolution: 1.8→73.37 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.583 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.085 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.85 Å2 / Biso mean: 17.695 Å2 / Biso min: 8.34 Å2
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Refinement step | Cycle: final / Resolution: 1.8→73.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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