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Yorodumi- PDB-3ret: Salicylate and Pyruvate Bound Structure of the Isochorismate-Pyru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ret | |||||||||
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Title | Salicylate and Pyruvate Bound Structure of the Isochorismate-Pyruvate Lyase K42E Mutant from Pseudomonas aerugionsa | |||||||||
Components | Salicylate biosynthesis protein pchBIsochorismate lyase | |||||||||
Keywords | LYASE / INTERTWINED DIMER / Mutase | |||||||||
Function / homology | Function and homology information pyochelin biosynthetic process / isochorismate lyase / isochorismate pyruvate lyase activity / carbon-oxygen lyase activity / salicylic acid biosynthetic process / chorismate metabolic process / chorismate mutase / chorismate mutase activity Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | |||||||||
Authors | Olucha, J. / Ouellette, A.N. / Luo, Q. / Lamb, A.L. | |||||||||
Citation | Journal: Biochemistry / Year: 2011 Title: pH Dependence of Catalysis by Pseudomonas aeruginosa Isochorismate-Pyruvate Lyase: Implications for Transition State Stabilization and the Role of Lysine 42. Authors: Olucha, J. / Ouellette, A.N. / Luo, Q. / Lamb, A.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ret.cif.gz | 52.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ret.ent.gz | 37.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ret.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/re/3ret ftp://data.pdbj.org/pub/pdb/validation_reports/re/3ret | HTTPS FTP |
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-Related structure data
Related structure data | 3remC 2h9dS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 11446.999 Da / Num. of mol.: 2 / Mutation: K42E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA4230, pchB / Plasmid: PET29B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: Q51507, Lyases; Carbon-carbon lyases; Other carbon-carbon lyases #2: Chemical | #3: Chemical | #4: 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: 1.74 Å3/Da / Density % sol: 29.41 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.6 Details: 0.004 M gly-gly, 0.100 M sodium acetate, 12% glycerol, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 1, 2009 / Details: Rh coated flat mirror, toroidal focusing mirror |
Radiation | Monochromator: Double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→25.89 Å / Num. all: 15734 / Num. obs: 13690 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.098 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 1.79→1.84 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2 / Num. unique all: 2186 / Rsym value: 0.375 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2H9D Resolution: 1.79→25.89 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.088 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.169 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.854 Å2
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Refinement step | Cycle: LAST / Resolution: 1.79→25.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.79→1.836 Å / Total num. of bins used: 20
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