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- PDB-4zu7: X-ray structure if the QdtA 3,4-ketoisomerase from Thermoanaeroba... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4zu7 | ||||||
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Title | X-ray structure if the QdtA 3,4-ketoisomerase from Thermoanaerobacterium thermosaccharolyticum, double mutant Y17R/R97H, in complex with TDP | ||||||
![]() | QdtA | ||||||
![]() | ISOMERASE / cupin isomerase 3-4-ketoisomerase | ||||||
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. / Vinogradov, E. / Gilbert, M. / Salinger, A.J. / Holden, H.M. | ||||||
![]() | ![]() Title: Bacterial Sugar 3,4-Ketoisomerases: Structural Insight into Product Stereochemistry. Authors: Thoden, J.B. / Vinogradov, E. / Gilbert, M. / Salinger, A.J. / 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 | ![]() | 244.6 KB | Display | ![]() |
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PDB format | ![]() | 197.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4zu4C ![]() 4zu5C ![]() 4o9eS S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 17140.793 Da / Num. of mol.: 8 / Mutation: Y17R, R97H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: qdtA / Plasmid: pET31 / Production host: ![]() ![]() #2: Chemical | ChemComp-TYD / #3: Chemical | ChemComp-PXN / ( | #4: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT THESE CONFLICTS MIGHT BE DUE TO STRAIN VARIANCE OR ERRORS IN THE INITIAL ...AUTHORS STATE THAT THESE CONFLICTS MIGHT BE DUE TO STRAIN VARIANCE OR ERRORS IN THE INITIAL SEQUENCING | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.48 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20-24% pentaerythrivol propoxylate (pp 5/4), 100 mM MES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Apr 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 52869 / Num. obs: 52869 / % possible obs: 90.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 1.8 / % possible all: 79.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4O9E Resolution: 2.3→29.28 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.921 / SU B: 8.311 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.416 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 41.576 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→29.28 Å
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Refine LS restraints |
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