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- PDB-5xse: Crystal structure of the 2-keto-3-deoxy-6-phosphogluconate aldola... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xse | ||||||
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Title | Crystal structure of the 2-keto-3-deoxy-6-phosphogluconate aldolase of Zymomonas mobilis ZM4 | ||||||
![]() | KHG/KDPG aldolase | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() (4S)-4-hydroxy-2-oxoglutarate aldolase activity / ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Seo, P.W. / Kim, J.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of the 2-keto-3-deoxy-6-phosphogluconate aldolase of Zymomonas mobilis ZM4 Authors: Seo, P.W. / Kim, J.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 254.5 KB | Display | ![]() |
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PDB format | ![]() | 207.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5xsfC ![]() 3onpS 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: 21526.324 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 31821 / ZM4 / CP4 / Gene: eda, kdgA, ZMO0997 / Production host: ![]() ![]() ![]() References: UniProt: Q00384, ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.74 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 25%(w/v) polyethylene glycol 8,000, 0.1M Bis-tris (pH 5.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.799→50 Å / Num. obs: 57557 / % possible obs: 98.5 % / Redundancy: 8.2 % / Rsym value: 0.077 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.8→1.88 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.43 / % possible all: 95.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3onp Resolution: 1.799→35.351 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 21.46 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.799→35.351 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 12.2895 Å / Origin y: -3.6222 Å / Origin z: -9.6936 Å
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Refinement TLS group | Selection details: all |