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Yorodumi- PDB-1xub: Structure and function of the phenazine biosynthetic protein PhzF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xub | ||||||
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Title | Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens | ||||||
Components | Phenazine biosynthesis protein phzF | ||||||
Keywords | BIOSYNTHETIC PROTEIN / phenazine biosynthesis | ||||||
Function / homology | Function and homology information trans-2,3-dihydro-3-hydroxyanthranilate isomerase / trans-2,3-dihydro-3-hydroxy-anthranilate isomerase activity / phenazine biosynthetic process Similarity search - Function | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / rigid body refinement of 1U1V / Resolution: 1.3 Å | ||||||
Authors | Blankenfeldt, W. / Kuzin, A.P. / Skarina, T. / Korniyenko, Y. / Tong, L. / Bayer, P. / Janning, P. / Thomashow, L.S. / Mavrodi, D.V. | ||||||
Citation | Journal: PROC.NATL.ACAD.SCI.USA / Year: 2004 Title: Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens Authors: Blankenfeldt, W. / Kuzin, A.P. / Skarina, T. / Korniyenko, Y. / Tong, L. / Bayer, P. / Janning, P. / Thomashow, L.S. / Mavrodi, D.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xub.cif.gz | 138.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xub.ent.gz | 107.8 KB | Display | PDB format |
PDBx/mmJSON format | 1xub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/1xub ftp://data.pdbj.org/pub/pdb/validation_reports/xu/1xub | HTTPS FTP |
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-Related structure data
Related structure data | 1sdjC 1u1vSC 1u1wC 1u1xC 1xuaC 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
#1: Protein | Mass: 32189.494 Da / Num. of mol.: 1 / Mutation: H74A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS / References: UniProt: Q51792 |
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#2: Chemical | ChemComp-SO4 / |
#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: 2.2 Å3/Da / Density % sol: 43.5 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 11% (w/v) PEG 3350, 0.1M Na Citrate, 0.2M (NH4)2 Sulfate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.007 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2004 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.007 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→20 Å / Num. all: 70364 / Num. obs: 63575 / % possible obs: 91.7 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 32 Å2 / Rsym value: 0.051 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.3→1.4 Å / Redundancy: 3 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.229 / % possible all: 69.5 |
-Processing
Software |
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Refinement | Method to determine structure: rigid body refinement of 1U1V Starting model: 1U1V Resolution: 1.3→19.1 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.98 / SU B: 1.006 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.045 / 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 mean: 24.128 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→19.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Origin x: 18.3438 Å / Origin y: 22.1671 Å / Origin z: 16.2598 Å
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Refinement TLS group |
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