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Yorodumi- PDB-5hpq: Crystal structure of cyclohexadienyl dehydratase from Pseudomonas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hpq | ||||||
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Title | Crystal structure of cyclohexadienyl dehydratase from Pseudomonas aeruginosa bound to acetate | ||||||
Components | Cyclohexadienyl dehydratase | ||||||
Keywords | LYASE / phenylalanine biosynthesis / cyclohexadienyl dehydratase / periplasmic binding protein | ||||||
Function / homology | Function and homology information arogenate dehydratase / arogenate dehydratase activity / prephenate dehydratase / prephenate dehydratase activity / L-phenylalanine biosynthetic process / periplasmic space Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Clifton, B.E. / Carr, P.D. / Jackson, C.J. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of cyclohexadienyl dehydratase from Pseudomonas aeruginosa bound to acetate Authors: Clifton, B.E. / Kaczmarski, J.A. / Carr, P.D. / Jackson, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hpq.cif.gz | 63.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hpq.ent.gz | 44.4 KB | Display | PDB format |
PDBx/mmJSON format | 5hpq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/5hpq ftp://data.pdbj.org/pub/pdb/validation_reports/hp/5hpq | HTTPS FTP |
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-Related structure data
Related structure data | 3kbrS 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: 29349.311 Da / Num. of mol.: 1 / Fragment: UNP residues 26-268 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria) Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: pheC, PA3475 / Plasmid: pDOTS7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q01269, prephenate dehydratase, arogenate dehydratase |
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#2: Chemical | ChemComp-ACT / |
#3: 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: 2.08 Å3/Da / Density % sol: 40.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 1 uL 10 mg/mL protein (20 mM TRIS pH 8.0, 100 mM NaCl, 0.5 mM DTT, 10% glycerol) + 1 uL 18% PEG 3350, 0.2 M ammonium acetate, 0.1 M TRIS pH 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 30, 2014 |
Radiation | Monochromator: Silicon double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→38.03 Å / Num. obs: 14471 / % possible obs: 97.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.05→2.11 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 1.6 / % possible all: 82.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KBR Resolution: 2.05→36.05 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.736 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.19 / 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: 30.129 Å2
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Refinement step | Cycle: 1 / Resolution: 2.05→36.05 Å
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