+Open data
-Basic information
Entry | Database: PDB / ID: 1pcm | ||||||
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Title | Enzyme-ligand complex of P. aeruginosa PMM/PGM | ||||||
Components | Phosphomannomutase | ||||||
Keywords | ISOMERASE / alpha/beta protein / phosphohexomutase / phosphoserine / enzyme-ligand complex / 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 / rigid body followed by regular refinement / Resolution: 1.9 Å | ||||||
Authors | Regni, C. / Tipton, P.A. / Beamer, L.J. | ||||||
Citation | Journal: Structure / Year: 2004 Title: Structural basis of diverse substrate recognition by the enzyme PMM/PGM from P. aeruginosa. Authors: Regni, C. / Naught, L. / 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 | 1pcm.cif.gz | 108.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pcm.ent.gz | 80.7 KB | Display | PDB format |
PDBx/mmJSON format | 1pcm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pc/1pcm ftp://data.pdbj.org/pub/pdb/validation_reports/pc/1pcm | HTTPS FTP |
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-Related structure data
Related structure data | 1p5dC 1p5gSC 1pcjC 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: 50430.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: ALGC OR PA5322 / Plasmid: PET3-A / Production host: Escherichia coli (E. coli) / Strain (production host): B121(DE3) / References: UniProt: P26276, phosphomannomutase |
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#2: Chemical | ChemComp-ZN / |
#3: Sugar | ChemComp-M6P / |
#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: 2.22 Å3/Da / Density % sol: 44.54 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Na K tartrate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop / 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: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 7, 2002 / Details: mirrors |
Radiation | Monochromator: Bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. all: 36023 / Num. obs: 35051 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.6 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 3.4 / % possible all: 97.8 |
Reflection | *PLUS Highest resolution: 1.9 Å / Rmerge(I) obs: 0.6 |
Reflection shell | *PLUS % possible obs: 97.8 % |
-Processing
Software |
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Refinement | Method to determine structure: rigid body followed by regular refinement Starting model: 1P5G Resolution: 1.9→24.85 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.045 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.149 / ESU R Free: 0.132 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.36 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→24.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.002 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: -49.8047 Å / Origin y: -18.2162 Å / Origin z: 10.8582 Å
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 24.9 Å / Rfactor Rfree: 0.2 / Rfactor Rwork: 0.17 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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