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Yorodumi- PDB-6mlf: Crystal structure of X. citri phosphoglucomutase in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mlf | |||||||||
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Title | Crystal structure of X. citri phosphoglucomutase in complex with 6-fluoro glucose 1-phosphate | |||||||||
Components | Phosphoglucomutase | |||||||||
Keywords | ISOMERASE / enzyme / carbohydrate biosynthesis | |||||||||
Function / homology | Function and homology information intramolecular phosphotransferase activity / carbohydrate metabolic process / magnesium ion binding Similarity search - Function | |||||||||
Biological species | Xanthomonas citri (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||
Authors | Beamer, L. / Stiers, K. | |||||||||
Funding support | United States, 1items
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Citation | Journal: J.Org.Chem. / Year: 2019 Title: Inhibitory Evaluation of alpha PMM/PGM fromPseudomonas aeruginosa: Chemical Synthesis, Enzyme Kinetics, and Protein Crystallographic Study. Authors: Zhu, J.S. / Stiers, K.M. / Soleimani, E. / Groves, B.R. / Beamer, L.J. / Jakeman, D.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mlf.cif.gz | 237.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mlf.ent.gz | 156.9 KB | Display | PDB format |
PDBx/mmJSON format | 6mlf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mlf_validation.pdf.gz | 811.5 KB | Display | wwPDB validaton report |
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Full document | 6mlf_full_validation.pdf.gz | 813.2 KB | Display | |
Data in XML | 6mlf_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 6mlf_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/6mlf ftp://data.pdbj.org/pub/pdb/validation_reports/ml/6mlf | HTTPS FTP |
-Related structure data
Related structure data | 6mlhC 6mlwC 6mnvC 5bmnS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 51217.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas citri (bacteria) / Gene: xanA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8PGN7 |
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#2: Sugar | ChemComp-JV4 / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.98 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 22% PEG 8000, 0.2 M MgCl2, 0.1 M Hepes, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00001 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Mar 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→46.33 Å / Num. obs: 51338 / % possible obs: 100 % / Redundancy: 13.6 % / Biso Wilson estimate: 22.26 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.65→1.68 Å / Rmerge(I) obs: 0.373 / Num. unique obs: 2512 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BMN Resolution: 1.75→46.33 Å / SU ML: 0.2323 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.5116 / Stereochemistry target values: GeoStd + Monomer Library
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→46.33 Å
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Refine LS restraints |
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LS refinement shell |
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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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