+Open data
-Basic information
Entry | Database: PDB / ID: 1ui9 | ||||||
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Title | Crystal analysis of chorismate mutase from thermus thermophilus | ||||||
Components | chorismate mutase | ||||||
Keywords | ISOMERASE / CHORISMATE MUTASE / SHIKIMATE PATHWAY / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information chorismate metabolic process / chorismate mutase / chorismate mutase activity / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Inagaki, E. / Kuramitsu, S. / Yokoyama, S. / Miyano, M. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: The crystal structure of chorismate mutase from thermus thermophilus Authors: Inagaki, E. / Kuramitsu, S. / Yokoyama, S. / Miyano, M. / Tahirov, T.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ui9.cif.gz | 39.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ui9.ent.gz | 26.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ui9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/1ui9 ftp://data.pdbj.org/pub/pdb/validation_reports/ui/1ui9 | HTTPS FTP |
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-Related structure data
Related structure data | 1ufyS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: -y, z-1/2, -x+1/2 and -z+1/2, -x, y+1/2. |
-Components
#1: Protein | Mass: 13726.764 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET 11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q84FH6, chorismate mutase | ||
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#2: Chemical | ChemComp-MES / | ||
#3: Chemical | ChemComp-GOL / #4: 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: 47.36 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 6.3 Details: Sodium malonate, MES, pH 6.3, Micro Batch, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jun 23, 2003 / Details: MIRRORS |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. all: 17108 / Num. obs: 16749 / % possible obs: 97.9 % / Observed criterion σ(I): -1 / Redundancy: 3.8 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.046 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.328 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UFY Resolution: 1.65→33.45 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1438630.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.7121 Å2 / ksol: 0.407688 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→33.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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