[English] 日本語
Yorodumi- PDB-6gt8: Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase Y132V,T1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gt8 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase Y132V,T157C variant | |||||||||
Components | 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase | |||||||||
Keywords | HYDROLASE / 2-keto-3-deoxygluconate / aldolase / Sulfolobus solfataricus | |||||||||
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 / (R,S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-tetrahydrodipicolinate synthase activity / glyoxylate catabolic process / cytosol Similarity search - Function | |||||||||
Biological species | Saccharolobus solfataricus (archaea) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.15 Å | |||||||||
Authors | Crennell, S.J. / Danson, M.J. / Royer, S. | |||||||||
Funding support | United Kingdom, 1items
| |||||||||
Citation | Journal: To Be Published Title: Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase Y132V,T157C variant Authors: Crennell, S.J. / Danson, M.J. / Royer, S. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6gt8.cif.gz | 226.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6gt8.ent.gz | 186.8 KB | Display | PDB format |
PDBx/mmJSON format | 6gt8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gt8_validation.pdf.gz | 454.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6gt8_full_validation.pdf.gz | 460.2 KB | Display | |
Data in XML | 6gt8_validation.xml.gz | 23 KB | Display | |
Data in CIF | 6gt8_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gt/6gt8 ftp://data.pdbj.org/pub/pdb/validation_reports/gt/6gt8 | HTTPS FTP |
-Related structure data
Related structure data | 6gsoC 6gv2C 1w37S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33028.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharolobus solfataricus (archaea) / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O54288, 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase #2: Sugar | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.56 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1M HEPES pH 6.0, 15% PEG 4K, 8% isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 29, 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: 3.15→51.54 Å / Num. obs: 13200 / % possible obs: 95.2 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 22 |
Reflection shell | Resolution: 3.15→3.37 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 5.3 / % possible all: 82 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1W37 Resolution: 3.15→36.93 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.64 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.15→36.93 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|