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Yorodumi- PDB-2h9d: Pyruvate-Bound Structure of the Isochorismate-Pyruvate Lyase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h9d | |||||||||
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Title | Pyruvate-Bound Structure of the Isochorismate-Pyruvate Lyase from Pseudomonas aerugionsa | |||||||||
Components | Salicylate biosynthesis protein pchBIsochorismate lyase | |||||||||
Keywords | LYASE / intertwined dimer | |||||||||
Function / homology | Function and homology information pyochelin biosynthetic process / isochorismate lyase / carbon-oxygen lyase activity / isochorismate pyruvate 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 / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Lamb, A.L. / Zaitseva, J. / Lu, J. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Two Crystal Structures of the Isochorismate Pyruvate Lyase from Pseudomonas aeruginosa. Authors: Zaitseva, J. / Lu, J. / Olechoski, K.L. / 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 | 2h9d.cif.gz | 90.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h9d.ent.gz | 68.6 KB | Display | PDB format |
PDBx/mmJSON format | 2h9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/2h9d ftp://data.pdbj.org/pub/pdb/validation_reports/h9/2h9d | HTTPS FTP |
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-Related structure data
Related structure data | 2h9cSC 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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Unit cell |
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Details | The asymmetric unit contains 2 dimers. Each dimer respresents one biological assembly. |
-Components
#1: Protein | Mass: 11447.064 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PchB / Plasmid: pET29b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q51507, Lyases; Carbon-carbon lyases; Other carbon-carbon lyases #2: Chemical | ChemComp-PYR / #3: Chemical | ChemComp-CA / | #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: 1.97 Å3/Da / Density % sol: 37.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM ADA, 25% PEG 3350, 0.15 M calcium acetate, 10% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 138 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 22, 2005 |
Radiation | Monochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→57.2 Å / Num. obs: 25853 / % possible obs: 95 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.066 |
Reflection shell | Resolution: 1.95→2.02 Å / Rmerge(I) obs: 0.405 / % possible all: 75.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2H9C Resolution: 1.95→57.2 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 28.6 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→57.2 Å
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Refine LS restraints |
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