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Yorodumi- PDB-4lu0: Crystal structure of 2-Keto-3-deoxy-D-manno-octulosonate-8-phosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lu0 | ||||||
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Title | Crystal structure of 2-Keto-3-deoxy-D-manno-octulosonate-8-phosphate synthase from Pseudomonas aeruginosa. | ||||||
Components | 2-dehydro-3-deoxyphosphooctonate aldolase | ||||||
Keywords | TRANSFERASE / TIM alpha-beta barrel / aldolase / phophoenol pyruvate / arabinose 5 phosphate / KDO8P | ||||||
Function / homology | Function and homology information Kdo2-lipid A biosynthetic process / Gram-negative-bacterium-type cell wall / 3-deoxy-8-phosphooctulonate synthase / 3-deoxy-8-phosphooctulonate synthase activity / keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / carbon utilization / lipopolysaccharide biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Asojo, O.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2013 Title: Structure of 2-keto-3-deoxy-D-manno-octulosonate-8-phosphate synthase from Pseudomonas aeruginosa. Authors: Nelson, S.K. / Kelleher, A. / Robinson, G. / Reiling, S. / Asojo, O.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lu0.cif.gz | 201.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lu0.ent.gz | 163.4 KB | Display | PDB format |
PDBx/mmJSON format | 4lu0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/4lu0 ftp://data.pdbj.org/pub/pdb/validation_reports/lu/4lu0 | HTTPS FTP |
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-Related structure data
Related structure data | 1g7vS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 32010.012 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) References: UniProt: Q9ZFK4, 3-deoxy-8-phosphooctulonate synthase #2: 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: 2.14 Å3/Da / Density % sol: 42.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M calcium acetate, and 0.1 M sodium cacodylate pH 6.5, 18% (w/v) polyethylene glycol 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å |
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Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jun 25, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→57.8 Å / Num. obs: 27850 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.243 / Net I/σ(I): 6.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G7V Resolution: 2.8→57.69 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.876 / SU B: 13.852 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 43.234 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→57.69 Å
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Refine LS restraints |
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