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Yorodumi- PDB-5iwe: E45Q mutant of phenazine biosynthesis protein PhzF in complex wit... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 5iwe | |||||||||
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| Title | E45Q mutant of phenazine biosynthesis protein PhzF in complex with (5R,6R)-6-azaniumyl-5-ethoxycyclohexa-1,3-diene-1-carboxylate | |||||||||
Components | Trans-2,3-dihydro-3-hydroxyanthranilate isomerase | |||||||||
Keywords | ISOMERASE / complex / substrate analogue | |||||||||
| Function / homology | Function and homology informationtrans-2,3-dihydro-3-hydroxyanthranilate isomerase / trans-2,3-dihydro-3-hydroxy-anthranilate isomerase activity / phenazine biosynthetic process / cytoplasm Similarity search - Function | |||||||||
| Biological species | Pseudomonas fluorescens (bacteria) | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | |||||||||
Authors | Diederich, C. / Blankenfeldt, W. | |||||||||
| Funding support | Germany, Austria, 2items
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Citation | Journal: Sci Rep / Year: 2017Title: Mechanisms and Specificity of Phenazine Biosynthesis Protein PhzF. Authors: Diederich, C. / Leypold, M. / Culka, M. / Weber, H. / Breinbauer, R. / Ullmann, G.M. / Blankenfeldt, W. | |||||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 5iwe.cif.gz | 181.3 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb5iwe.ent.gz | 147.1 KB | Display | PDB format |
| PDBx/mmJSON format | 5iwe.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 5iwe_validation.pdf.gz | 462.9 KB | Display | wwPDB validaton report |
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| Full document | 5iwe_full_validation.pdf.gz | 464.1 KB | Display | |
| Data in XML | 5iwe_validation.xml.gz | 15.3 KB | Display | |
| Data in CIF | 5iwe_validation.cif.gz | 22.3 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/5iwe ftp://data.pdbj.org/pub/pdb/validation_reports/iw/5iwe | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 1u1vS S: Starting model for refinement |
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| Similar structure data |
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Links
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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: 32255.576 Da / Num. of mol.: 1 / Mutation: E45Q Source method: isolated from a genetically manipulated source Details: The first 19 residues consist of the N-terminal expression tag and are neither natural nor visible in the structure Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: phzF / Production host: ![]() References: UniProt: Q51792, trans-2,3-dihydro-3-hydroxyanthranilate isomerase |
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-Non-polymers , 5 types, 249 molecules 








| #2: Chemical | ChemComp-W81 / ( | ||||||
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| #3: Chemical | | #4: Chemical | #5: Chemical | #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: 2.26 Å3/Da / Density % sol: 45.5 % |
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| Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.085M sodium acetate pH 4.6, 0.17M ammonium acetate, 25.5% (w/v) PEG 4000, 15% (v/v) glycerol, temperature 293.15K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
| Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2015 |
| Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
| Reflection | Resolution: 1.71→77.87 Å / Num. obs: 31593 / % possible obs: 99.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 8.9 |
| Reflection shell | Resolution: 1.71→1.74 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: 1U1V Resolution: 1.71→46.328 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.89 / Details: TLS-refinement
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| Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 1.71→46.328 Å
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| Refine LS restraints |
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| LS refinement shell |
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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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About Yorodumi



Pseudomonas fluorescens (bacteria)
X-RAY DIFFRACTION
Germany,
Austria, 2items
Citation










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