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Yorodumi- PDB-3r77: Crystal structure of the D38A mutant of isochorismatase PhzD from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r77 | ||||||
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Title | Crystal structure of the D38A mutant of isochorismatase PhzD from Pseudomonas fluorescens 2-79 in complex with 2-amino-2-desoxyisochorismate ADIC | ||||||
Components | Probable isochorismatase | ||||||
Keywords | HYDROLASE / isochorismatase / phenazine biosynthesis | ||||||
Function / homology | Function and homology information trans-2,3-dihydro-3-hydroxyanthranilic acid synthase / isochorismatase activity / phenazine biosynthetic process / : Similarity search - Function | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Li, Q.A. / Mavrodi, D.V. / Thomashow, L.S. / Roessle, M. / Blankenfeldt, W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Ligand Binding Induces an Ammonia Channel in 2-Amino-2-desoxyisochorismate (ADIC) Synthase PhzE. Authors: Li, Q.A. / Mavrodi, D.V. / Thomashow, L.S. / Roessle, M. / Blankenfeldt, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r77.cif.gz | 179.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r77.ent.gz | 144 KB | Display | PDB format |
PDBx/mmJSON format | 3r77.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3r77_validation.pdf.gz | 452.3 KB | Display | wwPDB validaton report |
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Full document | 3r77_full_validation.pdf.gz | 457.6 KB | Display | |
Data in XML | 3r77_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 3r77_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r7/3r77 ftp://data.pdbj.org/pub/pdb/validation_reports/r7/3r77 | 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
#1: Protein | Mass: 23248.461 Da / Num. of mol.: 2 / Mutation: D38A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: phzD / Plasmid: pET19modTEV / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: Q51790, isochorismatase #2: Chemical | #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: 2.14 Å3/Da / Density % sol: 42.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Na-cacodylate, 0.2 M Na-acetate, 25% (w/v) PEG 4000, soaking with 1 mM ADIC for 60 minutes, pH 6.5, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.542 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 11, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→49.653 Å / Num. obs: 31346 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.851 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 5.466 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.131 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.58 Å2 / Biso mean: 27.3776 Å2 / Biso min: 14.39 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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