+Open data
-Basic information
Entry | Database: PDB / ID: 1t9m | ||||||
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Title | X-ray crystal structure of phzG from pseudomonas aeruginosa | ||||||
Components | probable pyridoxamine 5'-phosphate oxidase | ||||||
Keywords | OXIDOREDUCTASE / phenazine / phzG / chorismate / pseudomonas | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-NH2 group of donors / pyridoxal 5'-phosphate synthase / phenazine biosynthetic process / pyridoxamine phosphate oxidase activity / pyridoxine biosynthetic process / FMN binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Parsons, J.F. / Eisenstein, E. / Ladner, J.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Structure of the phenazine biosynthesis enzyme PhzG. Authors: Parsons, J.F. / Calabrese, K. / Eisenstein, E. / Ladner, J.E. | ||||||
History |
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Remark 600 | HETEROGEN FMN 250 IS ASSOCIATED WITH CHAIN A. FMN 350 IS ASSOCIATED WITH CHAIN B. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t9m.cif.gz | 106.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t9m.ent.gz | 80.6 KB | Display | PDB format |
PDBx/mmJSON format | 1t9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1t9m_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1t9m_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1t9m_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 1t9m_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t9/1t9m ftp://data.pdbj.org/pub/pdb/validation_reports/t9/1t9m | HTTPS FTP |
-Related structure data
Related structure data | 1ty9C 1dnlS 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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Details | The biological assembly is a dimer and the dimer is contained in an asymmetric unit. |
-Components
#1: Protein | Mass: 24300.232 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: phzG / Plasmid: PET-28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) / References: UniProt: O69755 #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #5: 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 Å3/Da / Density % sol: 39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2M lithium sulfate, 0.1M tris, 25% (w/v) PEG 3350, pH 8.5, 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: Mar 21, 2003 / 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: 1.9→54 Å / Num. obs: 31579 / % possible obs: 99.7 % / Redundancy: 6 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 6 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 5.3 / Num. unique all: 5984 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1DNL Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.463 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.158 / 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: 25.574 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.002 Å / Total num. of bins used: 10 /
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