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- PDB-1mxs: Crystal structure of 2-keto-3-deoxy-6-phosphogluconate (KDPG) ald... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mxs | ||||||
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Title | Crystal structure of 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase from Pseudomonas putida. | ||||||
![]() | KDPG Aldolase | ||||||
![]() | LYASE / 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE / SULFATE / BETA-BARREL | ||||||
Function / homology | ![]() 2-dehydro-3-deoxy-phosphogluconate aldolase / 2-dehydro-3-deoxy-phosphogluconate aldolase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Watanabe, L. / Bell, B.J. / Lebioda, L. / Rios-Steiner, J.L. / Tulinsky, A. / Arni, R.K. | ||||||
![]() | ![]() Title: Structure of 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase from Pseudomonas putida. Authors: Bell, B.J. / Watanabe, L. / Rios-Steiner, J.L. / Tulinsky, A. / Lebioda, L. / Arni, R.K. #1: ![]() Title: Directed evolution of a new catalytic site in 2-keto-3-deoxy-6-phosphogluconate aldolase from Escherichia coli. Authors: Wymer, N. / Buchanan, L.V. / Henderson, D. / Mehta, N. / Botting, C.H. / Pocivavsek, L. / Fierke, C.A. / Toone, E.J. / Naismith, J.H. #2: ![]() Title: Covalent intermediate trapped in 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase structure at 1.95-A resolution Authors: Allard, J. / Grochulski, P. / Sygusch, J. #3: ![]() Title: The folding and quaternary structure of trimeric 2-keto-3-deoxy-6-phosphogluconic aldolase at 3.5-A resolution. Authors: Mavridis, I.M. / Tulinsky, A. #4: ![]() Title: Structure of 2-keto-3-deoxy-6-phosphogluconate aldolase at 2.8A resolution Authors: Mavridis, I.M. / Hatada, M.H. / Tulinsky, A. / Lebioda, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.6 KB | Display | ![]() |
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PDB format | ![]() | 39.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.6 KB | Display | ![]() |
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Full document | ![]() | 444 KB | Display | |
Data in XML | ![]() | 10.8 KB | Display | |
Data in CIF | ![]() | 14 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1eunS S: Starting model for refinement |
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Similar structure data |
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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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 24003.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P00885, 2-dehydro-3-deoxy-phosphogluconate aldolase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.82 Å3/Da / Density % sol: 67.84 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: microdialysis / pH: 3.5 Details: ammonium sulfate, KH2PO4, pH 3.5, MICRODIALYSIS, temperature 296K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: microdialysis | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 296 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Details: Yale/MSC mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→9.98 Å / Num. obs: 9901 / Biso Wilson estimate: 12.6 Å2 / Rsym value: 0.046 |
Reflection shell | Resolution: 2.2→50 Å / Num. unique all: 9901 / Rsym value: 0.046 |
Reflection | *PLUS % possible obs: 52.3 % / Num. measured all: 66178 / Rmerge(I) obs: 0.046 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1EUN Resolution: 2.2→9.98 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.9183 Å2 / ksol: 0.341747 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 34.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→9.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→50 Å / Rfactor Rfree error: 0.059 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 9999 Å / % reflection Rfree: 10 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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