[English] 日本語
![](img/lk-miru.gif)
- PDB-7c16: Crystal structure of a dinucleotide-binding protein (Y224A/Y246A)... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7c16 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a dinucleotide-binding protein (Y224A/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 | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 322 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 258.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 36.4 KB | Display | |
Data in CIF | ![]() | 53.5 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 ![]() 7c19C ![]() 7c1bC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||
2 | ![]()
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 1 - 394 / Label seq-ID: 3 - 396
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44320.598 Da / Num. of mol.: 2 / Mutation: Y224A, Y246A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 8 types, 557 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/CO2.gif)
![](data/chem/img/CO3.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/FGO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CO2.gif)
![](data/chem/img/CO3.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/FGO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-CO2 / #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-PEG / | #8: Chemical | #9: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.35 % / Description: Monoclinic |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / 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 | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() | |||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 22, 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 twin |
| |||||||||||||||||||||||||||
Reflection | Resolution: 1.9→60.84 Å / Num. obs: 71958 / % possible obs: 100 % / Redundancy: 4.1 % / CC1/2: 0.969 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.089 / Rrim(I) all: 0.18 / Net I/σ(I): 6.8 / Num. measured all: 294910 / Scaling rejects: 349 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 4 %
|
-Phasing
Phasing | Method: ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 7C0F Resolution: 1.9→58.52 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.902 / SU B: 3.569 / SU ML: 0.059 / SU R Cruickshank DPI: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.026 Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.91 Å2 / Biso mean: 18.485 Å2 / Biso min: 6.25 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→58.52 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Ens-ID: 1 / Number: 12512 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.947 Å / Rfactor Rfree error: 0
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|