+Open data
-Basic information
Entry | Database: PDB / ID: 5uxo | ||||||
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Title | Type II DAH7PS from Pseudomonas aeruginosa | ||||||
Components | Phospho-2-dehydro-3-deoxyheptonate aldolase | ||||||
Keywords | TRANSFERASE / DAH7PS / 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase / shikimate pathway | ||||||
Function / homology | Function and homology information 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / aromatic amino acid family biosynthetic process Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 Å | ||||||
Authors | Sterritt, O.W. / Jameson, G.B. / Parker, E.J. | ||||||
Citation | Journal: Biochemistry / Year: 2018 Title: A Pseudoisostructural Type II DAH7PS Enzyme from Pseudomonas aeruginosa: Alternative Evolutionary Strategies to Control Shikimate Pathway Flux. Authors: Sterritt, O.W. / Kessans, S.A. / Jameson, G.B. / Parker, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uxo.cif.gz | 99.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uxo.ent.gz | 77.8 KB | Display | PDB format |
PDBx/mmJSON format | 5uxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5uxo_validation.pdf.gz | 314.2 KB | Display | wwPDB validaton report |
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Full document | 5uxo_full_validation.pdf.gz | 318 KB | Display | |
Data in XML | 5uxo_validation.xml.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/5uxo ftp://data.pdbj.org/pub/pdb/validation_reports/ux/5uxo | 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 50197.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: PA2843 / Plasmid: pET28a / Details (production host): N-terminal His tag + linker / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9I000, 3-deoxy-7-phosphoheptulonate synthase |
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-Non-polymers , 5 types, 133 molecules
#2: Chemical | ChemComp-CO / | ||||
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#3: Chemical | ChemComp-PEP / | ||||
#4: Chemical | #5: Chemical | ChemComp-ACT / | #6: 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: 2.35 Å3/Da / Density % sol: 47.68 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M sodium acetate pH 5.5, 0.8 M sodium formate, 1 mM cobalt chloride, 1 mM phosphoenol pyruvate, 26 % PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→75.68 Å / Num. obs: 19777 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.992 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.056 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 1924 / CC1/2: 0.962 / Rpim(I) all: 0.156 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 2.35→75.68 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.899 / SU B: 8.065 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.404 / ESU R Free: 0.265 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.944 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→75.68 Å
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Refine LS restraints |
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