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Yorodumi- PDB-6aal: Crystal Structure of putative amino acid binding periplasmic ABC ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6aal | ||||||
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Title | Crystal Structure of putative amino acid binding periplasmic ABC transporter protein from Candidatus Liberibacter asiaticus in complex with Arginine | ||||||
Components | Putative amino acid-binding periplasmic ABC transporter protein | ||||||
Keywords | TRANSPORT PROTEIN / Periplasmic / Solute binding / Candidatus Liberibacter asiaticus / ABC transporter | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Liberibacter asiaticus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Kumar, P. / Kesari, P. / Ghosh, D.K. / Kumar, P. / Sharma, A.K. | ||||||
Citation | Journal: Febs J. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6aal.cif.gz | 110.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6aal.ent.gz | 84.9 KB | Display | PDB format |
PDBx/mmJSON format | 6aal.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6aal_validation.pdf.gz | 490.6 KB | Display | wwPDB validaton report |
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Full document | 6aal_full_validation.pdf.gz | 496.6 KB | Display | |
Data in XML | 6aal_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 6aal_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/6aal ftp://data.pdbj.org/pub/pdb/validation_reports/aa/6aal | HTTPS FTP |
-Related structure data
Related structure data | 6a80C 6a8sC 6aa1C 2ylnS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Liberibacter asiaticus (strain psy62) (bacteria) Strain: psy62 / Gene: CLIBASIA_05070 / Plasmid: pET28C / Production host: Escherichia coli (E. coli) / References: UniProt: C6XGT2 |
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-Non-polymers , 5 types, 101 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-ARG / | #5: Chemical | ChemComp-ACT / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.75 % / 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 pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→70.64 Å / Num. obs: 15666 / % possible obs: 98.6 % / Redundancy: 4.2 % / Biso Wilson estimate: 41.5 Å2 / Rsym value: 0.15 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.23 / Num. unique obs: 741 / Rsym value: 0.8 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YLN Resolution: 2.6→70.64 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.869 / SU B: 17.454 / SU ML: 0.36 / Cross valid method: THROUGHOUT / ESU R Free: 0.398 / Details: 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 mean: 40.787 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→70.64 Å
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Refine LS restraints |
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