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Yorodumi- PDB-1k35: Crystal Structure of Phosphomannomutase/Phosphoglucomutase from P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k35 | ||||||
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Title | Crystal Structure of Phosphomannomutase/Phosphoglucomutase from P.aeruginosa | ||||||
Components | Phosphomannomutase | ||||||
Keywords | ISOMERASE / alpha/beta protein / phosphoserine / enzyme-metal complex | ||||||
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 / MAD / Resolution: 2.2 Å | ||||||
Authors | Regni, C. / Tipton, P.A. / Beamer, L.J. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Crystal structure of PMM/PGM: an enzyme in the biosynthetic pathway of P. aeruginosa virulence factors. Authors: Regni, C. / Tipton, P.A. / 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 | 1k35.cif.gz | 97 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k35.ent.gz | 78.8 KB | Display | PDB format |
PDBx/mmJSON format | 1k35.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k35_validation.pdf.gz | 372.3 KB | Display | wwPDB validaton report |
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Full document | 1k35_full_validation.pdf.gz | 387.1 KB | Display | |
Data in XML | 1k35_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 1k35_validation.cif.gz | 19.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/1k35 ftp://data.pdbj.org/pub/pdb/validation_reports/k3/1k35 | HTTPS FTP |
-Related 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: 50805.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: AlgC / Plasmid: pET3-A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P26276, phosphomannomutase |
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#2: Chemical | ChemComp-ZN / |
#3: 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: 2.41 Å3/Da / Density % sol: 48.5 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Na, K tartrate, MOPS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Regni, C.A., (2000) Acta Crystallogr, D56, 761. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.979151 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979151 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. all: 24319 / Num. obs: 24319 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 43.1 Å2 / Rmerge(I) obs: 0.011 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 5.8 / % possible all: 98.7 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. measured all: 185144 / Rmerge(I) obs: 0.071 |
Reflection shell | *PLUS % possible obs: 98.7 % / Rmerge(I) obs: 0.333 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.2→40 Å / SU B: 11.49017 / SU ML: 0.2838 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.3702 / ESU R Free: 0.2621 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 43.135 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→40 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 40 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rfree: 0.276 / Rfactor Rwork: 0.234 | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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