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- PDB-1v5x: Crystal structure of Phosphoribosyl anthranilate isomerase from T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1v5x | ||||||
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Title | Crystal structure of Phosphoribosyl anthranilate isomerase from Thermus Thermophilus | ||||||
![]() | Phosphoribosylanthranilate isomerase | ||||||
![]() | ISOMERASE / alpha-beta barrel / TrpF / phosphoribosyl anthranilate isomerase / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | ![]() phosphoribosylanthranilate isomerase / phosphoribosylanthranilate isomerase activity / tryptophan biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Taka, J. / Kunishima, N. / Yutani, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Stabilization due to dimer formation of phosphoribosyl anthranilate isomerase from Thermus thermophilus HB8: X-ray Analysis and DSC experiments. Authors: Taka, J. / Ogasahara, K. / Jeyakanthan, J. / Kunishima, N. / Kuroishi, C. / Sugahara, M. / Yokoyama, S. / Yutani, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94 KB | Display | ![]() |
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PDB format | ![]() | 72.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.3 KB | Display | ![]() |
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Full document | ![]() | 444.6 KB | Display | |
Data in XML | ![]() | 20.4 KB | Display | |
Data in CIF | ![]() | 29.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nsjS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | The biological assembly is a dimer generated in the asymmetric unit. |
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Components
#1: Protein | Mass: 21977.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P83825, phosphoribosylanthranilate isomerase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.52 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 5.1 Details: Isopropanol, Sodium Acetate, pH 5.1, microbatch, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 8 / Method: batch method | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 3, 2003 / Details: mirrors |
Radiation | 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: 2→35 Å / Num. all: 35156 / Num. obs: 35156 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 29.43 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.076 / Net I/σ(I): 9.92 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 3 / Num. unique all: 3404 / Rsym value: 0.698 / % possible all: 99.4 |
Reflection | *PLUS Num. measured all: 307402 / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 99.4 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1NSJ Resolution: 2→35 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 44.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Rfactor Rfree error: 0.026
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Refinement | *PLUS % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |