[English] 日本語
Yorodumi- PDB-6ml0: Crystal structure of the periplasmic Lysine-, Arginine-, Ornithin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ml0 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) S69A mutant from Salmonella typhimurium | |||||||||||||||
Components | Lysine/arginine/ornithine-binding periplasmic protein | |||||||||||||||
Keywords | PROTEIN BINDING / Periplasmic Binding Protein / LAO / Thermodynamics / Protein Ligand Complex | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | Salmonella typhimurium (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | |||||||||||||||
Authors | Romero-Romero, S. / Vergara, R. / Espinoza-Perez, G. / Rodriguez-Romero, A. | |||||||||||||||
Funding support | Mexico, 4items
| |||||||||||||||
Citation | Journal: Febs J. / Year: 2020 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ml0.cif.gz | 76.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ml0.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ml0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ml0_validation.pdf.gz | 439.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6ml0_full_validation.pdf.gz | 439.8 KB | Display | |
Data in XML | 6ml0_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 6ml0_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/6ml0 ftp://data.pdbj.org/pub/pdb/validation_reports/ml/6ml0 | HTTPS FTP |
-Related structure data
Related structure data | 6mkuC 6mkwC 6mkxC 6ml9C 6mlaC 6mldC 6mleC 6mlgC 6mliC 6mljC 6mlnC 6mloC 6mlpC 6mlvC 2laoS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26042.314 Da / Num. of mol.: 1 / Mutation: S69A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: argT, STM2355 / Plasmid: pET12b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: P02911 |
---|---|
#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.84 % |
---|---|
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 |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 25, 2017 / Details: Osmic VariMax Cu-HF |
Radiation | Monochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→50 Å / Num. obs: 33775 / % possible obs: 99.3 % / Redundancy: 5.4 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 47.6 |
Reflection shell | Resolution: 1.68→1.71 Å / Mean I/σ(I) obs: 4 / Num. unique obs: 3103 / % possible all: 95.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2LAO Resolution: 1.68→33.57 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.87
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→33.57 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|