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- PDB-6ml9: Crystal structure of the periplasmic Lysine-, Arginine-, Ornithin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ml9 | |||||||||||||||
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Title | Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) D30A mutant from Salmonella typhimurium complexed with arginine | |||||||||||||||
![]() | Lysine/arginine/ornithine-binding periplasmic protein | |||||||||||||||
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Function / homology | ![]() | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() | |||||||||||||||
![]() | Romero-Romero, S. / Vergara, R. / Espinoza-Perez, G. / Rodriguez-Romero, A. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The interplay of protein-ligand and water-mediated interactions shape affinity and selectivity in the LAO binding protein. Authors: Vergara, R. / Romero-Romero, S. / Velazquez-Lopez, I. / Espinoza-Perez, G. / Rodriguez-Hernandez, A. / Pulido, N.O. / Sosa-Peinado, A. / Rodriguez-Romero, A. / Fernandez-Velasco, D.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 | ![]() | 152.9 KB | Display | ![]() |
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PDB format | ![]() | 120.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6mkuC ![]() 6mkwC ![]() 6mkxC ![]() 6ml0C ![]() 6mlaC ![]() 6mldC ![]() 6mleC ![]() 6mlgC ![]() 6mliC ![]() 6mljC ![]() 6mlnC ![]() 6mloC ![]() 6mlpC ![]() 6mlvC ![]() 1lafS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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: 26014.305 Da / Num. of mol.: 1 / Mutation: D30A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: argT, STM2355 / Plasmid: pET12b / Production host: ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-ARG / ![]() | ||||
#3: Chemical | ![]() #4: Chemical | ChemComp-GOL / | ![]() #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.37 % |
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Crystal grow![]() | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M Sodium acetate trihydrate 0.1 M Sodium cacodylate trihydrate 30% w/v Polyethylene glycol 8,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 19, 2018 / Details: Osmic VariMax Cu-HF |
Radiation | Monochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.68→50 Å / Num. obs: 25298 / % possible obs: 98.6 % / Redundancy: 8 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 38.3 |
Reflection shell | Resolution: 1.68→1.75 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 7.1 / Num. unique obs: 2382 / CC1/2: 0.857 / % possible all: 96 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1LAF Resolution: 1.687→38.114 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.63 / 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: 1.687→38.114 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 10.6533 Å / Origin y: 0.2107 Å / Origin z: -12.8335 Å
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Refinement TLS group | Selection details: all |