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Open data
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Basic information
Entry | Database: PDB / ID: 2v81 | ||||||
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Title | Native KDPGal structure | ||||||
![]() | 2-DEHYDRO-3-DEOXY-6-PHOSPHOGALACTONATE ALDOLASE | ||||||
![]() | LYASE / KDPGAL / ALDOLASE | ||||||
Function / homology | ![]() 2-dehydro-3-deoxy-6-phosphogalactonate aldolase / D-galactonate catabolic process / 2-dehydro-3-deoxy-6-phosphogalactonate aldolase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Naismith, J.H. | ||||||
![]() | ![]() Title: Characterization and crystal structure of Escherichia coli KDPGal aldolase. Authors: Walters, M.J. / Srikannathasan, V. / McEwan, A.R. / Naismith, J.H. / Fierke, C.A. / Toone, E.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 46.7 KB | Display | ![]() |
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PDB format | ![]() | 36.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 409.4 KB | Display | ![]() |
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Full document | ![]() | 410.7 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 12.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2v82C ![]() 2j6n ![]() 2j6q 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22489.225 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q6BF16, 2-dehydro-3-deoxy-6-phosphogalactonate aldolase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.86 Å3/Da / Density % sol: 67.89 % / Description: NONE |
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Crystal grow | pH: 5 / Details: pH 5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9871 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→59 Å / Num. obs: 12814 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 3 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 2.4→59.03 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.923 / SU B: 11.589 / SU ML: 0.139 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.192 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.53 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→59.03 Å
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Refine LS restraints |
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