+Open data
-Basic information
Entry | Database: PDB / ID: 1t6k | ||||||
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Title | Crystal structure of phzF from Pseudomonas fluorescens 2-79 | ||||||
Components | Phenazine biosynthesis protein phzF | ||||||
Keywords | ISOMERASE / phenazine / chorismate / phzF / enzyme | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Parsons, J.F. / Song, F. / Parsons, L. / Calabrese, K. / Eisenstein, E. / Ladner, J.E. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Structure and function of the phenazine biosynthesis protein PhzF from Pseudomonas fluorescens 2-79 Authors: Parsons, J.F. / Song, F. / Parsons, L. / Calabrese, K. / Eisenstein, E. / Ladner, J.E. | ||||||
History |
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Remark 600 | HETEROGEN THE COORDINATES CONTAIN THE MINOR CONFORMATION OF OG SER 213. THE SHORT CONTACT BETWEEN ...HETEROGEN THE COORDINATES CONTAIN THE MINOR CONFORMATION OF OG SER 213. THE SHORT CONTACT BETWEEN THIS ATOM AND O2 SO4 301 PROBABLY INDICATES THAT THE SULFATE ION POSITION IS PARTIALLY OCCUPIED BY A WATER MOLECULE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t6k.cif.gz | 71.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t6k.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 1t6k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/1t6k ftp://data.pdbj.org/pub/pdb/validation_reports/t6/1t6k | HTTPS FTP |
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-Related structure data
Related structure data | 1p9v S: Starting model for refinement |
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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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Details | The second molecule of the dimer can be generated by applying the matrix -0.50000 -0.86603 0.00000 -0.86603 0.50000 -0.00000 0.00000 -0.00000 -1.00000 and the vector 84.33016 48.68816 103.37299 |
-Components
#1: Protein | Mass: 30085.191 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: PHZF / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q51792 | ||
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#2: Chemical | #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: 2.35 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: Reservoir solution: 0.20 M ammonium sulfate, 0.10 M sodium citrate pH 5.6 and 18% (w/v) PEG 4000. The protein concentration was 17 mg/ml, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 24, 2004 / Details: MSC Blue Confocal Optics |
Radiation | Monochromator: MSC Blue Confocal Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→52 Å / Num. all: 27247 / Num. obs: 27247 / % possible obs: 99.7 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.89 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 4.7 / Num. unique all: 2593 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1P9V 1p9v Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.626 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 23.368 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 1.8 Å / Num. reflection Rwork: 3667 / Total num. of bins used: 10 |