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Yorodumi- PDB-1k2y: Crystal Structure of Phosphomannomutase/Phosphoglucomutase S108A ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k2y | ||||||
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Title | Crystal Structure of Phosphomannomutase/Phosphoglucomutase S108A mutant from P. aeruginosa | ||||||
Components | phosphomannomutase | ||||||
Keywords | ISOMERASE / ALPHA/BETA PROTEIN / ACTIVE-SITE MUTANT / ENZYME-LIGAND 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 / refinement of wild-type structure / Resolution: 1.75 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 | 1k2y.cif.gz | 108.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k2y.ent.gz | 82.3 KB | Display | PDB format |
PDBx/mmJSON format | 1k2y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/1k2y ftp://data.pdbj.org/pub/pdb/validation_reports/k2/1k2y | HTTPS FTP |
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-Related structure data
Related structure data | 1k35SC 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: 50334.352 Da / Num. of mol.: 1 / Mutation: S108A 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: Chemical | ChemComp-TLA / |
#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: 2.25 Å3/Da / Density % sol: 44.8 % | ||||||||||||||||||||||||||||||
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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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: Osmic confocal |
Radiation | Monochromator: OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→40 Å / Num. all: 49105 / Num. obs: 49105 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 33.22 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 1.75→1.81 Å / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 2.3 / % possible all: 98.8 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. measured all: 240203 |
Reflection shell | *PLUS % possible obs: 98.8 % |
-Processing
Software |
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Refinement | Method to determine structure: refinement of wild-type structure Starting model: Native protein, pdb entry 1k35 Resolution: 1.75→40 Å / SU B: 2.9191 / SU ML: 0.09446 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.10699 / ESU R Free: 0.10087 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 28.905 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→40 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Rfactor all: 0.17 / Rfactor Rfree: 0.196 / Rfactor Rwork: 0.169 | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_angle_deg / Dev ideal: 1.6 |