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Yorodumi- PDB-1xua: Structure and function of the phenazine biosynthetic protein PhzF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xua | ||||||
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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 / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / rigid body refinement of 1U1W / Resolution: 1.9 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 | 1xua.cif.gz | 133.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xua.ent.gz | 102.6 KB | Display | PDB format |
PDBx/mmJSON format | 1xua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xua_validation.pdf.gz | 454.8 KB | Display | wwPDB validaton report |
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Full document | 1xua_full_validation.pdf.gz | 459.9 KB | Display | |
Data in XML | 1xua_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | 1xua_validation.cif.gz | 39.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/1xua ftp://data.pdbj.org/pub/pdb/validation_reports/xu/1xua | HTTPS FTP |
-Related structure data
Related structure data | 1sdjC 1u1vC 1u1wSC 1u1xC 1xubC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 32256.561 Da / Num. of mol.: 2 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 #2: Chemical | #3: 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: 2.1 Å3/Da / Density % sol: 40.86 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 28% (w/v) PEG 4000, 0.1M Na-Citrate, 0.2M (NH4) Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 5, 2004 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 43122 / Num. obs: 43013 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 23 Å2 / Rsym value: 0.104 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.463 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: rigid body refinement of 1U1W Starting model: 1U1W Resolution: 1.9→19.8 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.804 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.125 / 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: 17.342 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→19.8 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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