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Yorodumi- PDB-6aa1: Crystal structure of putative amino acid binding periplasmic ABC ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6aa1 | ||||||
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Title | Crystal structure of putative amino acid binding periplasmic ABC transporter protein from Candidatus Liberibacter asiaticus bound with citrate | ||||||
Components | Putative amino acid-binding periplasmic ABC transporter protein | ||||||
Keywords | TRANSPORT PROTEIN / Candidatus Liberibacter asiaticus / periplasmic / ABC transporter / Solute binding / Citrate | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Liberibacter asiaticus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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 | 6aa1.cif.gz | 125.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6aa1.ent.gz | 97.4 KB | Display | PDB format |
PDBx/mmJSON format | 6aa1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6aa1_validation.pdf.gz | 507.5 KB | Display | wwPDB validaton report |
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Full document | 6aa1_full_validation.pdf.gz | 519.9 KB | Display | |
Data in XML | 6aa1_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 6aa1_validation.cif.gz | 35.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/6aa1 ftp://data.pdbj.org/pub/pdb/validation_reports/aa/6aa1 | HTTPS FTP |
-Related structure data
Related structure data | 6a80C 6a8sC 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 , 5 types, 307 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | ChemComp-PEG / | #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: 2.21 Å3/Da / Density % sol: 44.31 % / Description: Cubic |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 20% PEG 550, 0.1 M Sodium Citrate pH 5.0 |
-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: Mar 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976251 Å / Relative weight: 1 |
Reflection | Resolution: 1.857→70.773 Å / Num. obs: 42127 / % possible obs: 99.9 % / Redundancy: 8.9 % / Biso Wilson estimate: 25.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.05 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.857→1.889 Å / Redundancy: 8.8 % / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2069 / CC1/2: 0.664 / Rpim(I) all: 0.407 / Rrim(I) all: 1.213 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YLN Resolution: 1.86→70.77 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.224 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.019 Å2
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Refinement step | Cycle: 1 / Resolution: 1.86→70.77 Å
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Refine LS restraints |
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