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Yorodumi- PDB-6h2s: Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase T157V/D1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h2s | |||||||||
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Title | Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase T157V/D181Q/A198L variant, pyruvate complex | |||||||||
Components | 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase | |||||||||
Keywords | LYASE / aldolase | |||||||||
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 / 4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-tetrahydrodipicolinate synthase activity / glyoxylate catabolic process / carbohydrate metabolic process / cytosol Similarity search - Function | |||||||||
Biological species | Sulfolobus solfataricus (archaea) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.17 Å | |||||||||
Authors | Crennell, S.J. / Danson, M.J. / Royer, S. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase T157V/D181Q/A198L variant Authors: Crennell, S.J. / Danson, M.J. / Royer, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h2s.cif.gz | 465.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h2s.ent.gz | 388.6 KB | Display | PDB format |
PDBx/mmJSON format | 6h2s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/6h2s ftp://data.pdbj.org/pub/pdb/validation_reports/h2/6h2s | HTTPS FTP |
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-Related structure data
Related structure data | 6h2rC 1w37S 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 , 1 types, 4 molecules ABCD
#1: Protein | Mass: 33074.312 Da / Num. of mol.: 4 / Mutation: T157V, D181Q, A198L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O54288, UniProt: Q97U28*PLUS, 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase |
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-Non-polymers , 5 types, 745 molecules
#2: Chemical | ChemComp-PYR / #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | ChemComp-IPA / | #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: 2.3 Å3/Da / Density % sol: 46.63 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 0.1M HEPES pH 6.1, 11% PEG4K, 4% isopropanol, 0.1M pyruvate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 28, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→50 Å / Num. obs: 60596 / % possible obs: 95.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 2.17→2.21 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 4.59 / Num. unique obs: 2496 / % possible all: 79.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1W37 Resolution: 2.17→28.794 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.4 / 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: 2.17→28.794 Å
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Refine LS restraints |
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LS refinement shell |
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