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- PDB-8gtu: 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: 8gtu | ||||||
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Title | Crystal Structure of putative amino acid binding periplasmic ABC transporter protein from Candidatus Liberibacter asiaticus in complex with Clidinium | ||||||
![]() | Putative amino acid-binding periplasmic ABC transporter protein | ||||||
![]() | TRANSPORT PROTEIN / amino acid binding receptors / periplasmic amino acid binding protein / Candidatus Liberibacter asiaticus | ||||||
Function / homology | Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / periplasmic space / membrane / Chem-KG2 / Putative amino acid-binding periplasmic ABC transporter protein![]() | ||||||
Biological species | Liberibacter asiaticus | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lonare, S. / Sharma, M. / Sharma, A.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Identification and evaluation of potential inhibitor molecules against TcyA from Candidatus Liberibacter asiaticus. Authors: Lonare, S. / Sharma, M. / Dalal, V. / Gubyad, M. / Kumar, P. / Nath Gupta, D. / Pareek, A. / Tomar, S. / Kumar Ghosh, D. / Kumar, P. / Kumar Sharma, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 206.6 KB | Display | ![]() |
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PDB format | ![]() | 170 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8gu1C ![]() 6a80S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#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 / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES BUFFER, 2.5M AMMONIUM SULFATE, pH 6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→50.44 Å / Num. obs: 16502 / % possible obs: 99.9 % / Redundancy: 1.9 % / CC1/2: 0.99 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.56→2.56 Å / Num. unique obs: 1989 / CC1/2: 0.721 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6A80 Resolution: 2.56→50.44 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.86 / SU B: 27.497 / SU ML: 0.284 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
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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 max: 109.95 Å2 / Biso mean: 40.369 Å2 / Biso min: 14.05 Å2
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Refinement step | Cycle: final / Resolution: 2.56→50.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.564→2.63 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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