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Yorodumi- PDB-7c69: Crystal structure of beta-glycosides-binding protein of ABC trans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c69 | ||||||
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Title | Crystal structure of beta-glycosides-binding protein of ABC transporter in a closed state bound to sophorose | ||||||
Components | Sugar ABC transporter, periplasmic sugar-binding protein | ||||||
Keywords | SUGAR BINDING PROTEIN / Conformational dynamics / substrate-binding protein / Induced-fit mechanism / Two-step ligand binding / Venus Fly-trap mechanism | ||||||
Function / homology | Bacterial extracellular solute-binding protein / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / Bacterial extracellular solute-binding protein / Sugar ABC transporter, periplasmic sugar-binding protein Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å | ||||||
Authors | Kanaujia, S.P. / Chandravanshi, M. / Samanta, R. | ||||||
Funding support | India, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2020 Title: Conformational Trapping of a beta-Glucosides-Binding Protein Unveils the Selective Two-Step Ligand-Binding Mechanism of ABC Importers. Authors: Chandravanshi, M. / Samanta, R. / 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 | 7c69.cif.gz | 326.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c69.ent.gz | 263.4 KB | Display | PDB format |
PDBx/mmJSON format | 7c69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7c69_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7c69_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7c69_validation.xml.gz | 33.2 KB | Display | |
Data in CIF | 7c69_validation.cif.gz | 47.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/7c69 ftp://data.pdbj.org/pub/pdb/validation_reports/c6/7c69 | HTTPS FTP |
-Related structure data
Related structure data | 7c63SC 7c64C 7c66C 7c67C 7c68C 7c6fC 7c6gC 7c6hC 7c6iC 7c6jC 7c6kC 7c6lC 7c6mC 7c6nC 7c6rC 7c6tC 7c6vC 7c6wC 7c6xC 7c6yC 7c6zC 7c70C 7c71C 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 2 - 415 / Label seq-ID: 3 - 416
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-Components
#1: Protein | Mass: 46023.289 Da / Num. of mol.: 2 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: TTHB082 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53W80 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-CL / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.05 Å3/Da / Density % sol: 40.08 % / Description: Orthorhombic |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Ammonium sulphate, 35% PEG 8000 |
-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 19, 2019 / 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: 2.35→62.79 Å / Num. obs: 32179 / % possible obs: 99.9 % / Redundancy: 8.7 % / CC1/2: 0.984 / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.071 / Rrim(I) all: 0.214 / Net I/σ(I): 9.6 / Num. measured all: 279970 / Scaling rejects: 405 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-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: 7C63 Resolution: 2.35→55.06 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.879 / SU B: 17.236 / SU ML: 0.212 / SU R Cruickshank DPI: 0.6542 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.654 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.88 Å2 / Biso mean: 26.38 Å2 / Biso min: 1.99 Å2
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Refinement step | Cycle: final / Resolution: 2.35→55.06 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 12832 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.35→2.411 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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