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Yorodumi- PDB-3olp: Crystal structure of a bacterial phosphoglucomutase, an enzyme im... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3olp | ||||||
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Title | Crystal structure of a bacterial phosphoglucomutase, an enzyme important in the virulence of multiple human pathogens | ||||||
Components | Phosphoglucomutase | ||||||
Keywords | ISOMERASE / Phosphohexomutase / Phosphoglucomutase / Metal Binding / Enzyme | ||||||
Function / homology | Function and homology information phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) / phosphoglucomutase activity / carbohydrate metabolic process / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Beamer, L.J. / Mehra-Chaudhary, R. | ||||||
Citation | Journal: Proteins / Year: 2011 Title: Crystal structure of a bacterial phosphoglucomutase, an enzyme involved in the virulence of multiple human pathogens. Authors: Mehra-Chaudhary, R. / Mick, J. / Tanner, J.J. / Henzl, M.T. / 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 | 3olp.cif.gz | 422.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3olp.ent.gz | 344.7 KB | Display | PDB format |
PDBx/mmJSON format | 3olp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3olp_validation.pdf.gz | 452.1 KB | Display | wwPDB validaton report |
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Full document | 3olp_full_validation.pdf.gz | 461.8 KB | Display | |
Data in XML | 3olp_validation.xml.gz | 42.1 KB | Display | |
Data in CIF | 3olp_validation.cif.gz | 61 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/3olp ftp://data.pdbj.org/pub/pdb/validation_reports/ol/3olp | HTTPS FTP |
-Related structure data
Related structure data | 3na5C 2fuvS 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: 60897.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: pgm, STM0698 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 References: UniProt: Q8ZQW9, phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) #2: Chemical | #3: Chemical | #4: 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: 2.27 Å3/Da / Density % sol: 45.71 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Bis Tris, 0.2 M Magnesium Chloride, 25% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 22, 2008 / Details: beamline |
Radiation | Monochromator: beamline optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 78342 / % possible obs: 99 % / Redundancy: 3.6 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.8 / Num. unique all: 7760 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 2FUV Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.672 / SU ML: 0.086 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.131 / 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: 31.328 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 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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