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- PDB-1u1x: Structure and function of phenazine-biosynthesis protein PhzF fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1u1x | ||||||
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Title | Structure and function of phenazine-biosynthesis protein PhzF from Pseudomonas fluorescens 2-79 | ||||||
![]() | Phenazine biosynthesis protein phzF | ||||||
![]() | ISOMERASE / LYASE / phenazine biosynthesis / acid/base catalysis / closed form / substrate complex | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Blankenfeldt, W. / Kuzin, A.P. / Skarina, T. / Korniyenko, Y. / Tong, L. / Bayer, P. / Janning, P. / Thomashow, L.S. / Mavrodi, D.V. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.8 KB | Display | ![]() |
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PDB format | ![]() | 101.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.8 KB | Display | ![]() |
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Full document | ![]() | 454.1 KB | Display | |
Data in XML | ![]() | 26.1 KB | Display | |
Data in CIF | ![]() | 38.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1sdjC ![]() 1u1vSC ![]() 1u1wC ![]() 1xuaC ![]() 1xubC C: citing same article ( 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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Unit cell |
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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.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 0.1M Na-Citrate, 0.2M NH4-Acetate, 28% (w/v) PEG 4000, crystals induced with 10mM 3-hydroxyanthranilic acid (inhibitor), then cross-soaked in mother liquor containing 10mM HHA for 10 days, ...Details: 0.1M Na-Citrate, 0.2M NH4-Acetate, 28% (w/v) PEG 4000, crystals induced with 10mM 3-hydroxyanthranilic acid (inhibitor), then cross-soaked in mother liquor containing 10mM HHA for 10 days, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 24, 2004 / Details: Mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→20 Å / Num. all: 43151 / Num. obs: 43151 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 4.9 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.075 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.88→1.98 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 5.4 / Rsym value: 0.284 / % possible all: 95.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1u1v Resolution: 1.88→29.49 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.35 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / 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 mean: 17.396 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.88→29.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.88→1.929 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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