[English] 日本語
Yorodumi- PDB-6j9y: Crystal structure of ABC transporter alpha-glycoside-binding prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6j9y | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of ABC transporter alpha-glycoside-binding protein in complex with maltose | |||||||||
Components | ABC transporter, periplasmic substrate-binding proteinATP-binding cassette transporter | |||||||||
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: 1.63 Å | |||||||||
Authors | Kanaujia, S.P. / Chandravanshi, M. / Gogoi, P. | |||||||||
Funding support | India, 1items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6j9y.cif.gz | 114 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6j9y.ent.gz | 83.2 KB | Display | PDB format |
PDBx/mmJSON format | 6j9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/6j9y ftp://data.pdbj.org/pub/pdb/validation_reports/j9/6j9y | HTTPS FTP |
---|
-Related structure data
Related structure data | 6j9wSC 6jadC 6jagC 6jahC 6jaiC 6jalC 6jamC 6janC 6jaoC 6japC 6jaqC 6jarC 6jazC 6jb0C 6jb4C 6jbaC 6jbbC 6jbeC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
-Protein / Sugars , 2 types, 2 molecules A
#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): 4 / References: UniProt: Q5SLD7 |
---|---|
#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
-Non-polymers , 4 types, 578 molecules
#3: Chemical | ChemComp-CIT / |
---|---|
#4: Chemical | ChemComp-EDO / |
#5: Chemical | ChemComp-CO3 / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.54 % / Description: Tetragonal |
---|---|
Crystal grow | Temperature: 277 K / Method: microbatch / pH: 5 Details: 0.05 M Citric Acid, 0.05 M Bis-Tris Propane, 16% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 27, 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: 1.63→73.57 Å / Num. obs: 67774 / % possible obs: 100 % / Redundancy: 9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.033 / Rrim(I) all: 0.075 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.63→8.92 Å / Redundancy: 8 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 3302 / CC1/2: 0.97 / Rpim(I) all: 0.135 / Rrim(I) all: 0.278 / % possible all: 99.9 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6J9W Resolution: 1.63→73.57 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.081 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.066 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.71 Å2 / Biso mean: 17.239 Å2 / Biso min: 7.39 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.63→73.57 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.629→1.671 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|