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- PDB-1q6o: Structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bou... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1q6o | ||||||
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Title | Structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound L-gulonaet 6-phosphate | ||||||
![]() | 3-keto-L-gulonate 6-phosphate decarboxylase | ||||||
![]() | LYASE / BETA BARREL | ||||||
Function / homology | ![]() 3-dehydro-L-gulonate-6-phosphate decarboxylase / 3-dehydro-L-gulonate-6-phosphate decarboxylase activity / L-ascorbic acid catabolic process / orotidine-5'-phosphate decarboxylase activity / 'de novo' pyrimidine nucleobase biosynthetic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wise, E.L. / Yew, W.S. / Gerlt, J.A. / Rayment, I. | ||||||
![]() | ![]() Title: Structural Evidence for a 1,2-Enediolate Intermediate in the Reaction Catalyzed by 3-Keto-l-Gulonate 6-Phosphate Decarboxylase, a Member of the Orotidine 5'-Monophosphate Decarboxylase Suprafamily Authors: Wise, E.L. / Yew, W.S. / Gerlt, J.A. / Rayment, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 196.9 KB | Display | ![]() |
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PDB format | ![]() | 156.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 24.6 KB | Display | |
Data in CIF | ![]() | 37 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23603.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P39304, Lyases; Carbon-carbon lyases; Aldehyde-lyases #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 41.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 7 Details: 16% MePEG 2000, 50 mM BTP pH 7.0, 5 mM MgCl2, microbatch, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 3, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0247 Å / Relative weight: 1 |
Reflection | Resolution: 1.202→100 Å / Num. obs: 131568 / % possible obs: 92.4 % / Observed criterion σ(I): 2 / Net I/σ(I): 29.6 |
Reflection shell | Resolution: 1.202→1.24 Å / Mean I/σ(I) obs: 4.5 / % possible all: 69.7 |
Reflection | *PLUS Highest resolution: 1.2 Å / Num. obs: 142337 / Num. measured all: 931685 / Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS Highest resolution: 1.2 Å / % possible obs: 69.7 % / Rmerge(I) obs: 0.302 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.279 Å2
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Refinement step | Cycle: LAST / Resolution: 1.202→91.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.202→1.234 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 1.2 Å / Lowest resolution: 500 Å / Rfactor Rfree: 0.16 / Rfactor Rwork: 0.141 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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