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Yorodumi- PDB-3bjz: Crystal structure of Pseudomonas aeruginosa phosphoheptose isomerase -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bjz | ||||||
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Title | Crystal structure of Pseudomonas aeruginosa phosphoheptose isomerase | ||||||
Components | Phosphoheptose isomerase | ||||||
Keywords | ISOMERASE / SIS DOMAIN / alpha/beta PROTEIN / LIPOPOLYSACCHARIDE BIOSYNTHESIS / PSI / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / Carbohydrate metabolism / Cytoplasm | ||||||
Function / homology | Function and homology information D-sedoheptulose-7-phosphate isomerase / D-sedoheptulose 7-phosphate isomerase activity / D-glycero-D-manno-heptose 7-phosphate biosynthetic process / lipopolysaccharide core region biosynthetic process / carbohydrate derivative binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Walker, J.R. / Evdokimova, E. / Kudritska, M. / Osipiuk, J. / Joachimiak, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Structure and Function of Sedoheptulose-7-phosphate Isomerase, a Critical Enzyme for Lipopolysaccharide Biosynthesis and a Target for Antibiotic Adjuvants. Authors: Taylor, P.L. / Blakely, K.M. / de Leon, G.P. / Walker, J.R. / McArthur, F. / Evdokimova, E. / Zhang, K. / Valvano, M.A. / Wright, G.D. / Junop, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bjz.cif.gz | 144 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bjz.ent.gz | 121.6 KB | Display | PDB format |
PDBx/mmJSON format | 3bjz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bjz_validation.pdf.gz | 467.6 KB | Display | wwPDB validaton report |
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Full document | 3bjz_full_validation.pdf.gz | 474.8 KB | Display | |
Data in XML | 3bjz_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 3bjz_validation.cif.gz | 38.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/3bjz ftp://data.pdbj.org/pub/pdb/validation_reports/bj/3bjz | HTTPS FTP |
-Related structure data
Related structure data | 1x92C 2i22C 2i2wC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21862.973 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Species: Pseudomonas aeruginosa / Strain: PAO1 / 1C / PRS 101 / LMG 12228 / Gene: gmhA, PA4425 / Plasmid: Modified pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD(DE3) References: UniProt: Q9HVZ0, Isomerases; Intramolecular oxidoreductases; Interconverting aldoses and ketoses, and related compounds #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CL / | #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: 45.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25 % PEG 3350, 0.1M Ammonium sulfate, 0.1 M Bis-Tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jun 15, 2004 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40 Å / Num. all: 60161 / Num. obs: 60161 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Rsym value: 0.072 / Net I/σ(I): 29 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 5980 / Rsym value: 0.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→39.19 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.876 / SU B: 8.113 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.45 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: The Friedel pairs were used in phasing. 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: 35.062 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→39.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.46 Å / Total num. of bins used: 20
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