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Yorodumi- PDB-1w3t: Sulfolobus solfataricus 2-keto-3-deoxygluconate (KDG) aldolase co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w3t | ||||||||||||
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Title | Sulfolobus solfataricus 2-keto-3-deoxygluconate (KDG) aldolase complex with D-KDGal, D-Glyceraldehyde and pyruvate | ||||||||||||
Components | 2-KETO-3-DEOXY GLUCONATE ALDOLASE | ||||||||||||
Keywords | LYASE / ARCHAEAL METABOLISM / D-KDGAL / PYRUVATE / D- GLYCERALDEHYDE | ||||||||||||
Function / homology | Function and homology information 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 / carbohydrate metabolic process Similarity search - Function | ||||||||||||
Biological species | SULFOLOBUS SOLFATARICUS (archaea) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||||||||
Authors | Theodossis, A. / Walden, H. / Westwick, E.J. / Connaris, H. / Lamble, H.J. / Hough, D.W. / Danson, M.J. / Taylor, G.L. | ||||||||||||
Citation | Journal: J. Biol. Chem. / Year: 2004 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" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" 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 "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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w3t.cif.gz | 258.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w3t.ent.gz | 210 KB | Display | PDB format |
PDBx/mmJSON format | 1w3t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w3/1w3t ftp://data.pdbj.org/pub/pdb/validation_reports/w3/1w3t | HTTPS FTP |
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-Related structure data
Related structure data | 1w37SC 1w3iC 1w3nC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 8 molecules ABCD
#1: Protein | Mass: 33152.359 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: PET3-A / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O54288, 2-dehydro-3-deoxyglucarate aldolase #4: Sugar | ChemComp-3GR / |
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-Non-polymers , 4 types, 831 molecules
#2: Chemical | ChemComp-RSH / #3: Chemical | ChemComp-PYR / #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55.2 % |
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Crystal grow | pH: 6 Details: 0.1M HEPES PH6, 13% PEG4,000, 8% ISOPROPANOL, pH 6.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 20, 2004 |
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: 2.1→39.8 Å / Num. obs: 85931 / % possible obs: 99.9 % / Observed criterion σ(I): 5 / Redundancy: 7.8 % / Biso Wilson estimate: 21.16 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W37 Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.63 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.162 / 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: 21.08 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→40 Å
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Refine LS restraints |
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