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Yorodumi- PDB-1r9c: Crystal Structure of Fosfomycin Resistance Protein FosX from Meso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r9c | ||||||
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Title | Crystal Structure of Fosfomycin Resistance Protein FosX from Mesorhizobium Loti | ||||||
Components | glutathione transferase | ||||||
Keywords | TRANSFERASE / fosfomycin resistance protein / Mn binding / antibiotic resistance | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mesorhizobium loti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Fillgrove, K.L. / Pakhomova, S. / Newcomer, M.E. / Armstrong, R.N. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2003 Title: Mechanistic diversity of fosfomycin resistance in pathogenic microorganisms. Authors: Fillgrove, K.L. / Pakhomova, S. / Newcomer, M.E. / Armstrong, R.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r9c.cif.gz | 64.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r9c.ent.gz | 47.4 KB | Display | PDB format |
PDBx/mmJSON format | 1r9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r9c_validation.pdf.gz | 440.4 KB | Display | wwPDB validaton report |
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Full document | 1r9c_full_validation.pdf.gz | 441.8 KB | Display | |
Data in XML | 1r9c_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 1r9c_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r9/1r9c ftp://data.pdbj.org/pub/pdb/validation_reports/r9/1r9c | HTTPS FTP |
-Related structure data
Related structure data | 1lqpS S: Starting model for refinement |
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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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Details | The biological assembly is a dimer. |
-Components
#1: Protein | Mass: 16205.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mesorhizobium loti (bacteria) / Gene: fosfomycin resistance protein / Plasmid: pET20-b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q98GG1, dimethylallyltranstransferase #2: Chemical | #3: 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: 1.95 Å3/Da / Density % sol: 36.96 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG8000, Tris, Li2SO4, MnCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 19, 2002 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→30 Å / Num. obs: 21017 / % possible obs: 91.1 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.077 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.83→1.9 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 1263 / Rsym value: 0.414 / % possible all: 55.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1LQP Resolution: 1.83→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.676 / SU ML: 0.109 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.16 Å2
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Refinement step | Cycle: LAST / Resolution: 1.83→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.877 Å / 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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Refinement | *PLUS Rfactor Rfree: 0.243 / Rfactor Rwork: 0.201 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |