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- PDB-1w3i: Sulfolobus solfataricus 2-keto-3-deoxygluconate (KDG) aldolase co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1w3i | |||||||||
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Title | Sulfolobus solfataricus 2-keto-3-deoxygluconate (KDG) aldolase complex with pyruvate | |||||||||
![]() | 2-KETO-3-DEOXY GLUCONATE ALDOLASE | |||||||||
![]() | ALDOLASE / ARCHAEAL METABOLISM / PYRUVATE | |||||||||
Function / homology | ![]() 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase / 2-dehydro-3-deoxy-6-phosphogalactonate aldolase activity / 2-dehydro-3-deoxy-phosphogluconate aldolase activity / (R,S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-tetrahydrodipicolinate synthase activity / glyoxylate catabolic process / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Theodossis, A. / Walden, H. / Westwick, E.J. / Connaris, H. / Lamble, H.J. / Hough, D.W. / Danson, M.J. / Taylor, G.L. | |||||||||
![]() | ![]() Title: The structural basis for substrate promiscuity in 2-keto-3-deoxygluconate aldolase from the Entner-Doudoroff pathway in Sulfolobus solfataricus. Authors: Theodossis, A. / Walden, H. / Westwick, E.J. / Connaris, H. / Lamble, H.J. / Hough, D.W. / Danson, M.J. / Taylor, G.L. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA BA" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 259.8 KB | Display | ![]() |
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PDB format | ![]() | 212 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 484.7 KB | Display | ![]() |
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Full document | ![]() | 498.7 KB | Display | |
Data in XML | ![]() | 52.7 KB | Display | |
Data in CIF | ![]() | 76.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1w37SC ![]() 1w3nC ![]() 1w3tC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33021.168 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O54288, 2-dehydro-3-deoxyglucarate aldolase #2: Chemical | ChemComp-PYR / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.9 % |
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Crystal grow | pH: 6 Details: 0.1M HEPES PH6, 13% PEG4000, 8% ISOPROPANOL, pH 6.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 8, 2003 |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→39.8 Å / Num. obs: 157939 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 18.74 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.6 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1W37 Resolution: 1.7→40 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.83 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.101 / 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: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.9 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→40 Å
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