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Yorodumi- PDB-7c70: Crystal structure of beta-glycosides-binding protein (W67A) of AB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c70 | ||||||
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Title | Crystal structure of beta-glycosides-binding protein (W67A) of ABC transporter in an open-liganded state bound to gentiobiose | ||||||
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 | Function and homology information Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein Similarity search - Domain/homology | ||||||
Biological species | Thermus thermophilus HB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 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 | 7c70.cif.gz | 338.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c70.ent.gz | 270.3 KB | Display | PDB format |
PDBx/mmJSON format | 7c70.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/7c70 ftp://data.pdbj.org/pub/pdb/validation_reports/c7/7c70 | HTTPS FTP |
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-Related structure data
Related structure data | 7c63SC 7c64C 7c66C 7c67C 7c68C 7c69C 7c6fC 7c6gC 7c6hC 7c6iC 7c6jC 7c6kC 7c6lC 7c6mC 7c6nC 7c6rC 7c6tC 7c6vC 7c6wC 7c6xC 7c6yC 7c6zC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / 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: 0 / Auth seq-ID: 2 - 415 / Label seq-ID: 3 - 416
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-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 45908.156 Da / Num. of mol.: 2 / Mutation: W67A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / 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 |
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-Non-polymers , 10 types, 850 molecules
#3: Chemical | #4: Chemical | ChemComp-SO3 / | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-EDO / #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-PO4 / | #11: Chemical | ChemComp-IMD / | #12: Water | ChemComp-HOH / | |
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-Details
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: 1.93 Å3/Da / Density % sol: 36.36 % / Description: Monoclinic |
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Crystal grow | Temperature: 293 K / Method: microbatch / Details: 0.2 M Ammonium sulphate, 55% 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: Feb 11, 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: 1.63→49.53 Å / Num. obs: 85916 / % possible obs: 99 % / Redundancy: 7.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.031 / Rrim(I) all: 0.085 / Net I/σ(I): 15.9 | ||||||||||||||||||||||||||||||
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: 1.63→49.48 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.126 / SU ML: 0.055 / SU R Cruickshank DPI: 0.0882 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.09 / 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: 68.21 Å2 / Biso mean: 16.092 Å2 / Biso min: 6.53 Å2
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Refinement step | Cycle: final / Resolution: 1.63→49.48 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 13309 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.63→1.671 Å / Rfactor Rfree error: 0
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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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