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- PDB-7c1b: Crystal structure of a dinucleotide-binding protein (F79A/Y224A/Y... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7c1b | ||||||
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Title | Crystal structure of a dinucleotide-binding protein (F79A/Y224A/Y246A and deletion of residues 50-75) of ABC transporter (unbound form) | ||||||
![]() | Sugar ABC transporter, periplasmic sugar-binding protein | ||||||
![]() | TRANSPORT PROTEIN / c-di-GMP/AMP / Substrate-binding protein / Thermus thermophilus / tRNA synthesis and/or modification / Venus Fly-trap mechanism / UgpB | ||||||
Function / homology | ![]() maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / transmembrane transport Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kanaujia, S.P. / Chandravanshi, M. / Samanta, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and thermodynamic insights into the novel dinucleotide-binding protein of ABC transporter unveils its moonlighting function. 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 | ![]() | 157.1 KB | Display | ![]() |
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PDB format | ![]() | 121.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.2 KB | Display | ![]() |
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Full document | ![]() | 461.8 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7c0fSC ![]() 7c0kC ![]() 7c0lC ![]() 7c0oC ![]() 7c0rC ![]() 7c0sC ![]() 7c0tC ![]() 7c0uC ![]() 7c0vC ![]() 7c0wC ![]() 7c0xC ![]() 7c0yC ![]() 7c0zC ![]() 7c14C ![]() 7c15C ![]() 7c16C ![]() 7c19C 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
#1: Protein | Mass: 41554.344 Da / Num. of mol.: 1 / Mutation: F79A, Y224A, Y246A and deletion of residues 50-75 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-EDO / |
#3: Chemical | ChemComp-PEG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.17 % / Description: Orthorhombic |
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 6.5 Details: 0.2M ammonium sulphate, 0.1M sodium cacodylate pH 6.5, 30% 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: Dec 8, 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: 2.3→62.2 Å / Num. obs: 16950 / % possible obs: 100 % / Redundancy: 10.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.048 / Rrim(I) all: 0.157 / Net I/σ(I): 11.5 / Num. measured all: 181309 / Scaling rejects: 496 | ||||||||||||||||||||||||||||||
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: 7C0F Resolution: 2.3→62.2 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.876 / WRfactor Rfree: 0.2519 / WRfactor Rwork: 0.1827 / FOM work R set: 0.8125 / SU B: 15.515 / SU ML: 0.193 / SU R Cruickshank DPI: 0.3787 / SU Rfree: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.379 / ESU R Free: 0.27 / 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: 81.58 Å2 / Biso mean: 30.045 Å2 / Biso min: 10.7 Å2
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Refinement step | Cycle: final / Resolution: 2.3→62.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 26.2028 Å / Origin y: 16.3681 Å / Origin z: 14.2605 Å
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