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Yorodumi- PDB-6jam: Crystal structure of ABC transporter alpha-glycoside-binding muta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jam | |||||||||
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Title | Crystal structure of ABC transporter alpha-glycoside-binding mutant protein R356A in complex with trehalose | |||||||||
Components | ABC transporter, periplasmic substrate-binding protein | |||||||||
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: 1.63 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 | 6jam.cif.gz | 115 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jam.ent.gz | 84 KB | Display | PDB format |
PDBx/mmJSON format | 6jam.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jam_validation.pdf.gz | 897.8 KB | Display | wwPDB validaton report |
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Full document | 6jam_full_validation.pdf.gz | 899.9 KB | Display | |
Data in XML | 6jam_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 6jam_validation.cif.gz | 36.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/6jam ftp://data.pdbj.org/pub/pdb/validation_reports/ja/6jam | HTTPS FTP |
-Related structure data
Related structure data | 6j9wSC 6j9yC 6jadC 6jagC 6jahC 6jaiC 6jalC 6janC 6jaoC 6japC 6jaqC 6jarC 6jazC 6jb0C 6jb4C 6jbaC 6jbbC 6jbeC 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: 46081.883 Da / Num. of mol.: 1 / Mutation: R356A 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: Polysaccharide | alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose |
-Non-polymers , 5 types, 593 molecules
#3: Chemical | ChemComp-CIT / | ||||||
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#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-ACT / | #7: 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: 57.45 % / 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: Mar 4, 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: 1.63→73.55 Å / Num. obs: 67875 / % possible obs: 100 % / Redundancy: 18.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.026 / Rrim(I) all: 0.082 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 1.63→8.92 Å / Redundancy: 16.3 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 3277 / CC1/2: 0.953 / Rpim(I) all: 0.194 / Rrim(I) all: 0.567 / % possible all: 100 |
-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: 1.63→73.55 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.138 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.068 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: 84.98 Å2 / Biso mean: 19.422 Å2 / Biso min: 9.85 Å2
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Refinement step | Cycle: final / Resolution: 1.63→73.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.629→1.671 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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