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- PDB-6a80: Crystal Structure of putative amino acid binding periplasmic ABC ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6a80 | ||||||
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Title | Crystal Structure of putative amino acid binding periplasmic ABC transporter protein from Candidatus Liberibacter asiaticus in complex with cystine | ||||||
![]() | Putative amino acid-binding periplasmic ABC transporter protein | ||||||
![]() | TRANSPORT PROTEIN / Putative amino acid binding / Candidatus Liberibacter asiaticus / periplasmic domain | ||||||
Function / homology | ![]() | ||||||
Biological species | Liberibacter asiaticus | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumar, P. / Kesari, P. / Ghosh, D.K. / Kumar, P. / Sharma, A.K. | ||||||
![]() | ![]() Title: Crystal structures of a putative periplasmic cystine-binding protein from Candidatus Liberibacter asiaticus: insights into an adapted mechanism of ligand binding. Authors: Kumar, P. / Kesari, P. / Kokane, S. / Ghosh, D.K. / Kumar, P. / Sharma, A.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124.7 KB | Display | ![]() |
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PDB format | ![]() | 96.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6a8sC ![]() 6aa1C ![]() 6aalC ![]() 2ylnS 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 , 1 types, 2 molecules AB
#1: Protein | Mass: 27615.590 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: psy62 / Gene: CLIBASIA_05070 / Plasmid: pET28C / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 325 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CYS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CYS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-TRS / | #5: Chemical | ChemComp-ACT / #6: Chemical | ChemComp-CYS / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.51 % / Description: cubic |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 2M Ammonium sulphate, 0.1M Sodium acetate Trihydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976251 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→70.76 Å / Num. obs: 70624 / % possible obs: 99.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 26.46 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.018 / Rrim(I) all: 0.038 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.56→1.587 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3510 / CC1/2: 0.809 / Rpim(I) all: 0.5 / Rrim(I) all: 0.781 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2YLN Resolution: 1.56→70.76 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.178 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.091
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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 mean: 32.021 Å2
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Refinement step | Cycle: 1 / Resolution: 1.56→70.76 Å
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Refine LS restraints |
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