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Yorodumi- PDB-1r37: Alcohol dehydrogenase from sulfolobus solfataricus complexed with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r37 | ||||||
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Title | Alcohol dehydrogenase from sulfolobus solfataricus complexed with NAD(H) and 2-ethoxyethanol | ||||||
Components | NAD-dependent alcohol dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / archaeon / zinc / NAD(H) dependent / holoform | ||||||
Function / homology | Function and homology information alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / zinc ion binding Similarity search - Function | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Esposito, L. / Bruno, I. / Sica, F. / Raia, C.A. / Giordano, A. / Rossi, M. / Mazzarella, L. / Zagari, A. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Crystal structure of a ternary complex of the alcohol dehydrogenase from Sulfolobus solfataricus Authors: Esposito, L. / Bruno, I. / Sica, F. / Raia, C.A. / Giordano, A. / Rossi, M. / Mazzarella, L. / Zagari, A. #1: Journal: J.Mol.Biol. / Year: 2002 Title: Crystal structure of the alcohol dehydrogenase from the hyperthermophilic archaeon Sulfolobus solfataricus at 1.85 A resolution Authors: Esposito, L. / Sica, F. / Raia, C.A. / Giordano, A. / Rossi, M. / Mazzarella, L. / Zagari, A. #2: Journal: FEBS Lett. / Year: 2003 Title: Structural study of a single-point mutant of Sulfolobus solfataricus alcohol dehydrogenase with enhanced activity Authors: Esposito, L. / Bruno, I. / Sica, F. / Raia, C.A. / Giordano, A. / Rossi, M. / Mazzarella, L. / Zagari, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r37.cif.gz | 149.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r37.ent.gz | 116.9 KB | Display | PDB format |
PDBx/mmJSON format | 1r37.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r37_validation.pdf.gz | 997.8 KB | Display | wwPDB validaton report |
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Full document | 1r37_full_validation.pdf.gz | 1010.2 KB | Display | |
Data in XML | 1r37_validation.xml.gz | 29.5 KB | Display | |
Data in CIF | 1r37_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/1r37 ftp://data.pdbj.org/pub/pdb/validation_reports/r3/1r37 | HTTPS FTP |
-Related structure data
Related structure data | 1jvbS S: Starting model for refinement |
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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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Details | The biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operation: -x+1, y, -z+1 |
-Components
#1: Protein | Mass: 37615.523 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: HOLO-ENZYME FORM / Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: ADH or SSO2536 / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / Strain (production host): RB791 / References: UniProt: P39462, alcohol dehydrogenase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: 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: 2.47 Å3/Da / Density % sol: 50.2 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 40%(V/V) 2-ethoxyethanol, 100MM NA/K phosphate, 200MM NACL, 2MM NAD+(NADH), pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 296K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 23 ℃ / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 7, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→25 Å / Num. all: 29287 / Num. obs: 29287 / % possible obs: 89.5 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.071 / Mean I/σ(I) obs: 8.8 / Num. unique all: 1962 / % possible all: 60.8 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 25 Å / Num. measured all: 70105 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / % possible obs: 60.8 % / Mean I/σ(I) obs: 8.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JVB Resolution: 2.3→25 Å / Rfactor Rfree error: 0.006 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: This C2 crystal displays non-merohedral twinning. the two reciprocal lattices are related by a 180 degree rotation about the A axis. Spots from the dominant lattice (~70%) were indexed and ...Details: This C2 crystal displays non-merohedral twinning. the two reciprocal lattices are related by a 180 degree rotation about the A axis. Spots from the dominant lattice (~70%) were indexed and reduced; this dataset was used for the structure refinement.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.14 Å2 / ksol: 0.344 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.3 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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