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- PDB-7c0y: Crystal structure of a dinucleotide-binding protein (Y246A) of AB... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7c0y | ||||||
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Title | Crystal structure of a dinucleotide-binding protein (Y246A) of ABC transporter endogenously bound to uridylyl-3'-5'-phospho-guanosine (Form I) | ||||||
![]() | 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 | ![]() | 331.4 KB | Display | ![]() |
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PDB format | ![]() | 267.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 38.2 KB | Display | |
Data in CIF | ![]() | 57.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7c0fSC ![]() 7c0kC ![]() 7c0lC ![]() 7c0oC ![]() 7c0rC ![]() 7c0sC ![]() 7c0tC ![]() 7c0uC ![]() 7c0vC ![]() 7c0wC ![]() 7c0xC ![]() 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: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 0 - 393 / Label seq-ID: 2 - 395
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44412.691 Da / Num. of mol.: 2 / Mutation: Y246A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 741 molecules ![](data/chem/img/CO2.gif)
![](data/chem/img/PO3.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FGO.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO3.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FGO.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CO2 / #3: Chemical | ChemComp-PO3 / | #4: Chemical | #5: Chemical | #6: Chemical | #7: 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: 2.21 Å3/Da / Density % sol: 44.35 % / Description: Monoclinic |
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 6.5 Details: 0.2M ammonium phosphate, 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: Jul 15, 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: 1.7→56.19 Å / Num. obs: 83006 / % possible obs: 97.6 % / Redundancy: 4.5 % / CC1/2: 0.991 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.055 / Rrim(I) all: 0.123 / Net I/σ(I): 8.7 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 4.3 %
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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: 1.7→56.19 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.271 / SU ML: 0.074 / SU R Cruickshank DPI: 0.1147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.112 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: 70.96 Å2 / Biso mean: 19.443 Å2 / Biso min: 6.69 Å2
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Refinement step | Cycle: final / Resolution: 1.7→56.19 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 13005 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.7→1.73 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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