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Yorodumi- PDB-6a8s: Crystal Structure of the putative amino acid-binding periplasmic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a8s | ||||||
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Title | Crystal Structure of the putative amino acid-binding periplasmic ABC transporter protein from Candidatus Liberibacter asiaticus in complex with Cysteine | ||||||
Components | Putative amino acid-binding periplasmic ABC transporter protein | ||||||
Keywords | TRANSPORT PROTEIN / Candidatus Liberibacter asiaticus / Periplasmic / Solute Binding / Cysteine | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Liberibacter asiaticus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 | 6a8s.cif.gz | 118.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a8s.ent.gz | 91.2 KB | Display | PDB format |
PDBx/mmJSON format | 6a8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6a8s_validation.pdf.gz | 519.7 KB | Display | wwPDB validaton report |
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Full document | 6a8s_full_validation.pdf.gz | 529.7 KB | Display | |
Data in XML | 6a8s_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 6a8s_validation.cif.gz | 31.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/6a8s ftp://data.pdbj.org/pub/pdb/validation_reports/a8/6a8s | HTTPS FTP |
-Related structure data
Related structure data | 6a80C 6aa1C 6aalC 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 , 7 types, 208 molecules
#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-TRS / | #5: Chemical | #6: Chemical | #7: Chemical | #8: 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: 2.22 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: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976251 Å |
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: 2.05→70.89 Å / Num. obs: 31433 / % possible obs: 99.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 35 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.071 / Rrim(I) all: 0.147 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3028 / CC1/2: 0.702 / Rpim(I) all: 0.452 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YLN Resolution: 2.05→36.885 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.71 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→36.885 Å
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Refine LS restraints |
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LS refinement shell |
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