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Yorodumi- PDB-3bkq: Structure of the P368G mutant of PMM/PGM in complex with its substrate -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bkq | ||||||
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Title | Structure of the P368G mutant of PMM/PGM in complex with its substrate | ||||||
Components | Phosphomannomutase/phosphoglucomutase | ||||||
Keywords | ISOMERASE / ALPHA/BETA PROTEIN / PHOSPHOHEXOMUTASE / PHOSPHOSERINE / ENZYME-LIGAND COMPLEX / ENZYME-METAL COMPLEx / Alginate biosynthesis / Lipopolysaccharide biosynthesis / Magnesium / Metal-binding / Multifunctional enzyme / Phosphoprotein | ||||||
Function / homology | Function and homology information phosphomannomutase / phosphomannomutase activity / phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) / phosphoglucomutase activity / alginic acid biosynthetic process / O antigen biosynthetic process / GDP-mannose biosynthetic process / lipopolysaccharide core region biosynthetic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / refinement / Resolution: 2.05 Å | ||||||
Authors | Mehra-Chaudhary, R. / Beamer, L.J. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Backbone flexibility, conformational change, and catalysis in a phosphohexomutase from Pseudomonas aeruginosa. Authors: Schramm, A.M. / Mehra-Chaudhary, R. / Furdui, C.M. / Beamer, L.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bkq.cif.gz | 104.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bkq.ent.gz | 78.3 KB | Display | PDB format |
PDBx/mmJSON format | 3bkq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bkq_validation.pdf.gz | 718.3 KB | Display | wwPDB validaton report |
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Full document | 3bkq_full_validation.pdf.gz | 720.2 KB | Display | |
Data in XML | 3bkq_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 3bkq_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/3bkq ftp://data.pdbj.org/pub/pdb/validation_reports/bk/3bkq | HTTPS FTP |
-Related structure data
Related structure data | 3c04C 1p5gS 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: 50390.266 Da / Num. of mol.: 1 / Mutation: P368G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: algC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P26276, phosphomannomutase, phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) |
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#2: Sugar | ChemComp-G1P / |
#3: Chemical | ChemComp-ZN / |
#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: 2.28 Å3/Da / Density % sol: 45.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: NA,K tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Nov 15, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→44.2 Å / Num. obs: 29408 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.69 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 3.1 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: refinement Starting model: PDB entry 1P5G Resolution: 2.05→44.2 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.929 / SU B: 11.759 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.539 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→44.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 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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