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Yorodumi- PDB-6jbe: Crystal structure of ABC transporter alpha-glycoside-binding muta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jbe | ||||||
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Title | Crystal structure of ABC transporter alpha-glycoside-binding mutant protein W287A in complex with glucose | ||||||
Components | ABC transporter, periplasmic substrate-binding proteinATP-binding cassette transporter | ||||||
Keywords | SUGAR BINDING PROTEIN / Carbohydrate-bindingsite / 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: 1.75 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 | 6jbe.cif.gz | 112.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jbe.ent.gz | 82.7 KB | Display | PDB format |
PDBx/mmJSON format | 6jbe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/6jbe ftp://data.pdbj.org/pub/pdb/validation_reports/jb/6jbe | HTTPS FTP |
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-Related structure data
Related structure data | 6j9wSC 6j9yC 6jadC 6jagC 6jahC 6jaiC 6jalC 6jamC 6janC 6jaoC 6japC 6jaqC 6jarC 6jazC 6jb0C 6jb4C 6jbaC 6jbbC 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 46052.867 Da / Num. of mol.: 1 / Mutation: W287A 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 (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q5SLD7 |
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#2: Sugar | ChemComp-GLC / |
-Non-polymers , 6 types, 579 molecules
#3: Chemical | ChemComp-CIT / | ||||||||
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#4: Chemical | #5: Chemical | ChemComp-PEG / | #6: Chemical | ChemComp-EDO / | #7: Chemical | ChemComp-CO2 / | #8: 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: 2.89 Å3/Da / Density % sol: 57.44 % / 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, 16% 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: Apr 23, 2018 / 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: 1.75→73.43 Å / Num. obs: 52985 / % possible obs: 97 % / Redundancy: 12.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.037 / Rrim(I) all: 0.099 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.75→9.09 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 2590 / CC1/2: 0.918 / Rpim(I) all: 0.238 / Rrim(I) all: 0.652 / % possible all: 88.3 |
-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: 6J9W Resolution: 1.75→73.43 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.71 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.088 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: 87.36 Å2 / Biso mean: 19.767 Å2 / Biso min: 9.52 Å2
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Refinement step | Cycle: final / Resolution: 1.75→73.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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