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- PDB-7c6w: Crystal structure of beta-glycosides-binding protein (W177X) of A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7c6w | ||||||
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Title | Crystal structure of beta-glycosides-binding protein (W177X) of ABC transporter in a closed state bound to laminaritetraose | ||||||
![]() | Sugar ABC transporter, periplasmic sugar-binding protein | ||||||
![]() | SUGAR BINDING PROTEIN / Conformational dynamics / substrate-binding protein / Induced-fit mechanism / Two-step ligand binding / Venus Fly-trap mechanism | ||||||
Function / homology | ![]() maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kanaujia, S.P. / Chandravanshi, M. / Samanta, R. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 182 KB | Display | ![]() |
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PDB format | ![]() | 141.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 741.8 KB | Display | ![]() |
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Full document | ![]() | 744.9 KB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 30.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7c63SC ![]() 7c64C ![]() 7c66C ![]() 7c67C ![]() 7c68C ![]() 7c69C ![]() 7c6fC ![]() 7c6gC ![]() 7c6hC ![]() 7c6iC ![]() 7c6jC ![]() 7c6kC ![]() 7c6lC ![]() 7c6mC ![]() 7c6nC ![]() 7c6rC ![]() 7c6tC ![]() 7c6vC ![]() 7c6xC ![]() 7c6yC ![]() 7c6zC ![]() 7c70C ![]() 7c71C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 45906.211 Da / Num. of mol.: 1 / Mutation: K174R, N175T, S176P, W177del, D178R, V179T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 6 types, 325 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/SO2.gif)
![](data/chem/img/CO3.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO2.gif)
![](data/chem/img/CO3.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CL / | ||||
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#4: Chemical | ChemComp-SO2 / | ||||
#5: Chemical | ChemComp-CO3 / | ||||
#6: Chemical | #7: Chemical | ChemComp-PO4 / | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.16 % / Description: Orthorhombic |
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Crystal grow | Temperature: 293 K / Method: microbatch / Details: 0.2 M Ammonium sulphate, 40% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 29, 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: 1.88→58.11 Å / Num. obs: 32582 / % possible obs: 98.5 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.031 / Rrim(I) all: 0.087 / Net I/σ(I): 15.2 / Num. measured all: 240945 / Scaling rejects: 201 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7C63 Resolution: 1.88→54.51 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.919 / SU B: 7.491 / SU ML: 0.117 / SU R Cruickshank DPI: 0.1668 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.158 / 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: 86.34 Å2 / Biso mean: 27.766 Å2 / Biso min: 10.15 Å2
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Refinement step | Cycle: final / Resolution: 1.88→54.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.88→1.929 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 22.6896 Å / Origin y: -0.996 Å / Origin z: -14.9499 Å
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