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- PDB-7c0k: Crystal structure of a dinucleotide-binding protein of ABC transp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7c0k | ||||||
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Title | Crystal structure of a dinucleotide-binding protein of ABC transporter endogenously bound to uridylyl-3'-5'-phospho-guanosine (Form II) | ||||||
![]() | 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. | ||||||
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 | ![]() | 337 KB | Display | ![]() |
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PDB format | ![]() | 270.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 39.2 KB | Display | |
Data in CIF | ![]() | 58.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7c0fSC ![]() 7c0lC ![]() 7c0oC ![]() 7c0rC ![]() 7c0sC ![]() 7c0tC ![]() 7c0uC ![]() 7c0vC ![]() 7c0wC ![]() 7c0xC ![]() 7c0yC ![]() 7c0zC ![]() 7c14C ![]() 7c15C ![]() 7c16C ![]() 7c19C ![]() 7c1bC 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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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: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 0 - 394 / Label seq-ID: 2 - 396
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44504.785 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 14 types, 685 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CO2.gif)
![](data/chem/img/PO2.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/BGQ.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/FGO.gif)
![](data/chem/img/CO3.gif)
![](data/chem/img/PO3.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CO2.gif)
![](data/chem/img/PO2.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/BGQ.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/FGO.gif)
![](data/chem/img/CO3.gif)
![](data/chem/img/PO3.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-CO2 / #5: Chemical | #6: Chemical | ChemComp-PO4 / | #7: Chemical | ChemComp-EDO / #8: Chemical | #9: Chemical | ChemComp-GOL / #10: Chemical | ChemComp-BGQ / | #11: Chemical | ChemComp-PG4 / | #12: Chemical | #13: Chemical | #14: Chemical | ChemComp-PO3 / | #15: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.7 % / Description: Monoclinic |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M ammonium phosphate, 0.1M sodium cacodylate pH6.5, 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: Apr 13, 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: 1.8→46.57 Å / Num. obs: 84314 / % possible obs: 99.9 % / Redundancy: 4.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.041 / Rrim(I) all: 0.086 / Net I/σ(I): 12.3 / Num. measured all: 361385 / Scaling rejects: 24 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 4.2 %
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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: 1.8→46.57 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.725 / SU ML: 0.046 / SU R Cruickshank DPI: 0.0209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.021 / ESU R Free: 0.02 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.55 Å2 / Biso mean: 21.452 Å2 / Biso min: 7.95 Å2
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Refinement step | Cycle: final / Resolution: 1.8→46.57 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 12840 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.8→1.847 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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