+Open data
-Basic information
Entry | Database: PDB / ID: 5uxm | ||||||
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Title | Type II DAH7PS from Pseudomonas aeruginosa with Trp bound | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.54 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 | 5uxm.cif.gz | 114.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uxm.ent.gz | 83.8 KB | Display | PDB format |
PDBx/mmJSON format | 5uxm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5uxm_validation.pdf.gz | 470 KB | Display | wwPDB validaton report |
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Full document | 5uxm_full_validation.pdf.gz | 472 KB | Display | |
Data in XML | 5uxm_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 5uxm_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/5uxm ftp://data.pdbj.org/pub/pdb/validation_reports/ux/5uxm | HTTPS FTP |
-Related structure data
Related structure data | 5uxnC 5uxoC 2b7oS 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 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) magic References: UniProt: Q9I000, 3-deoxy-7-phosphoheptulonate synthase |
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-Non-polymers , 6 types, 327 molecules
#2: Chemical | ChemComp-PEP / | ||||||
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#3: Chemical | ChemComp-TRP / | ||||||
#4: Chemical | #5: Chemical | ChemComp-CO / | #6: Chemical | #7: 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: 2.37 Å3/Da / Density % sol: 48.13 % / Description: rectangular rod |
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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 Temp details: Temperature controlled |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 26, 2016 |
Radiation | Monochromator: Double Crystal SI(111) water cooled sagittal focusing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→75.79 Å / Num. obs: 70122 / % possible obs: 99.6 % / Redundancy: 7 % / Biso Wilson estimate: 13.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.044 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.54→1.57 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.122 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3437 / CC1/2: 0.702 / Rpim(I) all: 0.452 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B7O Resolution: 1.54→75.79 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.782 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.08 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.135 Å2
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Refinement step | Cycle: 1 / Resolution: 1.54→75.79 Å
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Refine LS restraints |
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