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- PDB-2yw3: Crystal Structure Analysis of the 4-hydroxy-2-oxoglutarate aldola... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yw3 | ||||||
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Title | Crystal Structure Analysis of the 4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-deoxyphosphogluconate aldolase from TTHB1 | ||||||
![]() | 4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-deoxyphosphogluconate aldolase | ||||||
![]() | LYASE / aldolase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | ![]() 2-dehydro-3-deoxy-phosphogluconate aldolase / 2-dehydro-3-deoxy-phosphogluconate aldolase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kawano, Y. / Hashimoto, K. / Kamiya, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystal Structure Analysis of the 4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-deoxyphosphogluconate aldolase from TTHB1 Authors: Kawano, Y. / Hashimoto, K. / Kamiya, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 253.2 KB | Display | ![]() |
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PDB format | ![]() | 204.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2yw4C ![]() 1mxsS C: citing same article ( S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21745.330 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q53W90, 2-dehydro-3-deoxy-phosphogluconate aldolase #2: Chemical | ChemComp-PO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.48 % |
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Crystal grow | Temperature: 301 K / Method: vapor diffusion, hanging drop / pH: 4.1 Details: 0.4M Potassium sodium tartrate tetrahydrate, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 301K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 12, 2005 |
Radiation | Monochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97937 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→35.6 Å / Num. all: 145847 / Num. obs: 145847 / % possible obs: 86.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 11.39 |
Reflection shell | Resolution: 1.67→1.73 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 3.52 / Num. unique all: 11116 / % possible all: 65.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1MXS Resolution: 1.67→35.58 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.727 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.103 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.695 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→35.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.669→1.712 Å / Total num. of bins used: 20
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