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- PDB-4zu5: Crystal structure of the QdtA 3,4-Ketoisomerase from Thermoanaero... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4zu5 | ||||||
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Title | Crystal structure of the QdtA 3,4-Ketoisomerase from Thermoanaerobacterium thermosaccharolyticum, apo form | ||||||
![]() | QdtA | ||||||
![]() | ISOMERASE / cupin / 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 | ![]() | 75.5 KB | Display | ![]() |
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PDB format | ![]() | 54.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 837.1 KB | Display | ![]() |
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Full document | ![]() | 842.9 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 18.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4zu4C ![]() 4zu7C ![]() 4o9eS 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
#1: Protein | Mass: 17165.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: qdtA / Plasmid: pET31 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-PXN / ( | #4: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THE FOLLOWING: ALA 52-SER, PHE 94 - LEU, LEU 95 - VAL, AND CYS 116 - TYR, WE BELIEVE ...AUTHORS 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: 3.06 Å3/Da / Density % sol: 59.8 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 18-22% pentaerythrivol propoxylate (5/4), 100 mM Homo-pipes |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Jul 13, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 37504 / Num. obs: 37504 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.4 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 44.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 1.7 / % possible all: 87.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4O9E Resolution: 1.8→38.81 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.073 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.116 / 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: 40.345 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→38.81 Å
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Refine LS restraints |
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