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Yorodumi- PDB-2d8d: Structure of Chorismate Mutase (Form I) from Thermus Thermophilus HB8 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d8d | ||||||
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Title | Structure of Chorismate Mutase (Form I) from Thermus Thermophilus HB8 | ||||||
Components | phospho-2-dehydro-3-deoxyheptonate aldolase/chorismate mutase | ||||||
Keywords | ISOMERASE / Chorismate / Dimer / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information chorismate metabolic process / chorismate mutase / chorismate mutase activity / 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / aldehyde-lyase activity / aromatic amino acid family biosynthetic process Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | ||||||
Authors | Bagautdinov, B. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Structure of Chorismate Mutase from Thermus Thermophilus HB8 Authors: Bagautdinov, B. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d8d.cif.gz | 53.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d8d.ent.gz | 37.6 KB | Display | PDB format |
PDBx/mmJSON format | 2d8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/2d8d ftp://data.pdbj.org/pub/pdb/validation_reports/d8/2d8d | HTTPS FTP |
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-Related structure data
Related structure data | 2d8eC 1ecmS C: citing same article (ref.) 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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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a dimer |
-Components
#1: Protein | Mass: 10738.213 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: AROAG / Plasmid: pET 11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q72LN8, UniProt: Q5SLA5*PLUS, chorismate mutase #2: Chemical | ChemComp-CL / | #3: 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: 1.86 Å3/Da / Density % sol: 33.77 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 6.1 Details: PEG 4K, MES 0.1M, NaOH, Mg Chloride 0.05M, pH 6.1, microbatch, 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: MARRESEARCH / Detector: CCD / Date: Jun 22, 2005 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→40 Å / Num. all: 57615 / Num. obs: 56929 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 9.648 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.051 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.15→1.19 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 2.6 / Num. unique all: 5091 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ECM Resolution: 1.15→29.62 Å / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 14.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.15→29.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.15→1.19 Å / Rfactor Rfree error: 0.02
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