+Open data
-Basic information
Entry | Database: PDB / ID: 4uxd | ||||||
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Title | 2-keto 3-deoxygluconate aldolase from Picrophilus torridus | ||||||
Components | 2-DEHYDRO-3-DEOXY-D-GLUCONATE/2-DEHYDRO-3-DEOXY-PHOSPHOGLUCONATE ALDOLASE | ||||||
Keywords | LYASE / TIM BARREL | ||||||
Function / homology | Function and homology information 2-dehydro-3-deoxy-6-phosphogalactonate aldolase / 2-dehydro-3-deoxy-D-gluconate aldolase / 2-dehydro-3-deoxy-D-gluconate aldolase activity / 2-dehydro-3-deoxy-6-phosphogalactonate aldolase activity / Lyases; Carbon-carbon lyases; Aldehyde-lyases / 2-dehydro-3-deoxy-phosphogluconate aldolase / 2-dehydro-3-deoxy-phosphogluconate aldolase activity / aldehyde-lyase activity / glucose catabolic process Similarity search - Function | ||||||
Biological species | PICROPHILUS TORRIDUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Priftis, A. / Zaitsev, V. / Reher, M. / Johnsen, U. / Danson, M.J. / Taylor, G.L. / Schoenheit, P. / Crennell, S.J. | ||||||
Citation | Journal: Biochemistry / Year: 2018 Title: Insights into the Substrate Specificity of Archaeal Entner-Doudoroff Aldolases: The Structures of Picrophilus torridus 2-Keto-3-deoxygluconate Aldolase and Sulfolobus solfataricus 2-Keto-3- ...Title: Insights into the Substrate Specificity of Archaeal Entner-Doudoroff Aldolases: The Structures of Picrophilus torridus 2-Keto-3-deoxygluconate Aldolase and Sulfolobus solfataricus 2-Keto-3-deoxy-6-phosphogluconate Aldolase in Complex with 2-Keto-3-deoxy-6-phosphogluconate. Authors: Zaitsev, V. / Johnsen, U. / Reher, M. / Ortjohann, M. / Taylor, G.L. / Danson, M.J. / Schonheit, P. / Crennell, S.J. #1: Journal: J.Bacteriol. / Year: 2010 Title: The Nonphosphorylative Entner-Doudoroff Pathway in the Thermoacidophilic Euryarchaeon Picrophilus Torridus Involves a Novel 2-Keto-3-Deoxygluconate- Specific Aldolase. Authors: Reher, M. / Fuhrer, T. / Bott, M. / Schonheit, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uxd.cif.gz | 237.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uxd.ent.gz | 193 KB | Display | PDB format |
PDBx/mmJSON format | 4uxd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uxd_validation.pdf.gz | 523.7 KB | Display | wwPDB validaton report |
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Full document | 4uxd_full_validation.pdf.gz | 535.8 KB | Display | |
Data in XML | 4uxd_validation.xml.gz | 44.5 KB | Display | |
Data in CIF | 4uxd_validation.cif.gz | 61.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/4uxd ftp://data.pdbj.org/pub/pdb/validation_reports/ux/4uxd | HTTPS FTP |
-Related structure data
Related structure data | 6g3zC 1xkyS 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: 34095.848 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PICROPHILUS TORRIDUS (archaea) / Strain: DSM 9790 / JCM 10055 / NBRC 100828 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIL References: UniProt: Q6KZI8, 2-dehydro-3-deoxy-D-gluconate aldolase , 2-dehydro-3-deoxy-phosphogluconate aldolase, 2-dehydro-3-deoxy-6-phosphogalactonate aldolase |
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-Non-polymers , 6 types, 369 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-PEG / | #6: Chemical | ChemComp-PGE / | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | KDGA_PICTO IS INCOMPLETE.THE SEQUENCE AS DEPOSITED AS Q6KZI8 IS SHORTER THAN THE CORRECT PTO1279 ...KDGA_PICTO IS INCOMPLETE |
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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: 2.49 Å3/Da / Density % sol: 50.58 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: PROTEIN AT 4.2MG/ML MIXED 1:1 WITH (0.085 M HEPES SODIUM BUFFER PH 7.5, 8.5% V/V 2-PROPANOL, 17% W/V PEG 4000, 15% V/V GLYCEROL (ANHYDROUS)) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 |
Detector | Type: SATURN 944PLUS / Detector: CCD / Date: Mar 26, 2009 / Details: OSMIC BLUE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→28.58 Å / Num. obs: 36955 / % possible obs: 86.6 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.25 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.65 / % possible all: 83.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XKY Resolution: 2.5→28.58 Å / SU ML: 0.37 / σ(F): 1.33 / Phase error: 30.03 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→28.58 Å
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Refine LS restraints |
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LS refinement shell |
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