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Yorodumi- PDB-6mlw: Crystal structure of X. citri phosphoglucomutase in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mlw | ||||||
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Title | Crystal structure of X. citri phosphoglucomutase in complex with 2-fluoro mannosyl-1-methyl-phosphonic acid | ||||||
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: 1.9 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 | 6mlw.cif.gz | 234.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mlw.ent.gz | 153.7 KB | Display | PDB format |
PDBx/mmJSON format | 6mlw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mlw_validation.pdf.gz | 795.5 KB | Display | wwPDB validaton report |
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Full document | 6mlw_full_validation.pdf.gz | 797.9 KB | Display | |
Data in XML | 6mlw_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 6mlw_validation.cif.gz | 37.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/6mlw ftp://data.pdbj.org/pub/pdb/validation_reports/ml/6mlw | HTTPS FTP |
-Related structure data
Related structure data | 6mlfC 6mlhC 6mnvC 5bmnS C: citing same article (ref.) 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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-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 (E. coli) / References: UniProt: Q8PGN7 |
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#2: Chemical | ChemComp-MG / |
#3: Sugar | ChemComp-JVA / |
#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: 2.15 Å3/Da / Density % sol: 42.92 % |
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Crystal grow | Temperature: 293 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 |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.000001 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Jan 31, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000001 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→57.64 Å / Num. obs: 33637 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 22.18 Å2 / CC1/2: 0.991 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2097 / CC1/2: 0.334 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5bmn Resolution: 1.9→42.44 Å / SU ML: 0.2807 / Cross valid method: THROUGHOUT / σ(F): 0.32 / Phase error: 25.6538
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→42.44 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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