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Yorodumi- PDB-5l9s: Structure of Agrobacterium tumefaciens C58 strain PBP AttC in ope... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l9s | ||||||
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Title | Structure of Agrobacterium tumefaciens C58 strain PBP AttC in open unliganded conformation | ||||||
Components | ABC transporter, substrate binding protein (Mannopine) | ||||||
Keywords | TRANSPORT PROTEIN / periplasmic binding protein ABC transporter | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Agrobacterium fabrum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | ||||||
Authors | Marty, L. / Morera, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Structural Basis for High Specificity of Amadori Compound and Mannopine Opine Binding in Bacterial Pathogens. Authors: Marty, L. / Vigouroux, A. / Aumont-Nicaise, M. / Dessaux, Y. / Faure, D. / Morera, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l9s.cif.gz | 271.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l9s.ent.gz | 220.3 KB | Display | PDB format |
PDBx/mmJSON format | 5l9s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l9s_validation.pdf.gz | 461.4 KB | Display | wwPDB validaton report |
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Full document | 5l9s_full_validation.pdf.gz | 466.9 KB | Display | |
Data in XML | 5l9s_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 5l9s_validation.cif.gz | 34 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/5l9s ftp://data.pdbj.org/pub/pdb/validation_reports/l9/5l9s | HTTPS FTP |
-Related structure data
Related structure data | 5l9gSC 5l9iC 5l9lC 5l9oC 5l9pC 5lomC 6hqhC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37275.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria) Gene: attC, Atu5129 / Production host: Escherichia coli (E. coli) / References: UniProt: A9CLM6 #2: Chemical | ChemComp-ACT / | #3: Chemical | ChemComp-EDO / | #4: 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: 46.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 40% PEG 4K, 0.1M MES pH 6.5, 0.2M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→50 Å / Num. obs: 24641 / % possible obs: 99 % / Redundancy: 5.1 % / Biso Wilson estimate: 64.25 Å2 / Rsym value: 0.115 / Net I/σ(I): 11.57 |
Reflection shell | Resolution: 2.49→2.64 Å / Rsym value: 1.259 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5L9G Resolution: 2.49→28.59 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.928 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.564 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.589 / SU Rfree Blow DPI: 0.263 / SU Rfree Cruickshank DPI: 0.266
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Displacement parameters | Biso mean: 65.75 Å2
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Refine analyze | Luzzati coordinate error obs: 0.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.49→28.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.49→2.6 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
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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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