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Yorodumi- PDB-2fn1: Crystal structures of Yersinia enterocolitica salicylate synthase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fn1 | |||||||||
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Title | Crystal structures of Yersinia enterocolitica salicylate synthase (Irp9) in complex with the reaction products salicylate and pyruvate | |||||||||
Components | salicylate synthetase, Irp9 | |||||||||
Keywords | TRANSCRIPTION / Yersinia enterocolitica / Irp9 / salicylate synthase / salicylate | |||||||||
Function / homology | Function and homology information isochorismate synthase activity / oxo-acid-lyase activity / carbon-oxygen lyase activity / siderophore biosynthetic process / tryptophan biosynthetic process / magnesium ion binding Similarity search - Function | |||||||||
Biological species | Yersinia enterocolitica (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Kerbarh, O. / Chirgadze, D.Y. / Blundell, T.L. / Abell, C. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Crystal Structures of Yersinia enterocolitica Salicylate Synthase and its Complex with the Reaction Products Salicylate and Pyruvate. Authors: Kerbarh, O. / Chirgadze, D.Y. / Blundell, T.L. / Abell, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fn1.cif.gz | 177.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fn1.ent.gz | 136.6 KB | Display | PDB format |
PDBx/mmJSON format | 2fn1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fn1_validation.pdf.gz | 473.4 KB | Display | wwPDB validaton report |
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Full document | 2fn1_full_validation.pdf.gz | 482.9 KB | Display | |
Data in XML | 2fn1_validation.xml.gz | 33.3 KB | Display | |
Data in CIF | 2fn1_validation.cif.gz | 47.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/2fn1 ftp://data.pdbj.org/pub/pdb/validation_reports/fn/2fn1 | HTTPS FTP |
-Related structure data
Related structure data | 2fn0C 1i1qS 1i7qS 1qdlS 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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Details | The biological assembly is the dimer present in the asymmetric unit |
-Components
#1: Protein | Mass: 48308.910 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Strain: 8081 / Gene: IRP9 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: GenBank: 5420055, UniProt: Q9X9I8*PLUS #2: Chemical | #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: 2.37 Å3/Da / Density % sol: 48.21 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M magnesium acetate tetrahydrate, 0.1M sodium cacodylate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 21, 2005 / Details: Rigaku Max Flux mirrors |
Radiation | Monochromator: Rigaku Max Flux mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 52602 / Num. obs: 49446 / % possible obs: 94 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2.5 / Redundancy: 4.8 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.299 / Num. unique all: 3453 / Rsym value: 0.299 / % possible all: 88.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: composite search probe from 1QDL, 1I7Q and 1I1Q Resolution: 2.1→27.37 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.006 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.232 / ESU R Free: 0.2 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.63 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→27.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.15 Å / Total num. of bins used: 20
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