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- PDB-4o9e: Crystal structure of QdtA, a sugar 3,4-ketoisemerase from Thermoa... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4o9e | ||||||
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Title | Crystal structure of QdtA, a sugar 3,4-ketoisemerase from Thermoanaerobacterium thermosaccharolyticum in complex with TDP | ||||||
![]() | QdtA | ||||||
![]() | ISOMERASE / cupin / 3 / 4-ketoisomerase / TDP-sugar binding | ||||||
Function / homology | ![]() Sugar 3,4-ketoisomerase QdtA, cupin domain / WxcM-like, C-terminal / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Thoden, J.B. / Holden, H.M. | ||||||
![]() | ![]() Title: The molecular architecture of QdtA, a sugar 3,4-ketoisomerase from Thermoanaerobacterium thermosaccharolyticum. Authors: Thoden, J.B. / Holden, H.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.9 KB | Display | ![]() |
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PDB format | ![]() | 56.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4o9gC ![]() 2pa7S C: citing same article ( 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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Unit cell |
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Components on special symmetry positions |
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Details | Biological dimer is composed of chains A+B |
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Components
#1: Protein | Mass: 17165.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: E207-71 / Gene: qdtA / Plasmid: pET31 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-TDR / | #4: Chemical | ChemComp-4TD / ( | #5: Water | ChemComp-HOH / | Sequence details | AUTHOR STATE THE FOLLOWING: ALA 52-> SER, PHE 94 -> LEU, LEU 95 ->VAL, AND CYS 116 -> TYR WE ...AUTHOR STATE THE FOLLOWING: ALA 52-> SER, PHE 94 -> LEU, LEU 95 ->VAL, AND CYS 116 -> TYR WE BELIEVE ARE SEQUENCING | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 22-28% pentaerythritol propoxylate, 100 mM HEPPS, 10 mM TDP, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Jan 9, 2009 / Details: montel mirrors |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→38.83 Å / Num. all: 28352 / Num. obs: 28352 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 3.7 / Num. unique all: 2040 / Rsym value: 0.282 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2PA7 Resolution: 2→38.83 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.939 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.148 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.695 Å2
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Refinement step | Cycle: LAST / Resolution: 2→38.83 Å
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Refine LS restraints |
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