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Yorodumi- PDB-1rjw: CRYSTAL STRUCTURE OF NAD(+)-DEPENDENT ALCOHOL DEHYDROGENASE FROM ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rjw | ||||||
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Title | CRYSTAL STRUCTURE OF NAD(+)-DEPENDENT ALCOHOL DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILUS STRAIN LLD-R | ||||||
Components | Alcohol dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / NAD / ZINC / ALCOHOL / DEHYDROGENASE / TETRAMER | ||||||
Function / homology | Function and homology information alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / zinc ion binding Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Ceccarelli, C. / Bahnson, B.J. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Crystal Structure and Amide H/D Exchange of Binary Complexes of Alcohol Dehydrogenase from Bacillus stearothermophilus: Insight into Thermostability and Cofactor Binding Authors: Ceccarelli, C. / Liang, Z.X. / Strickler, M. / Prehna, G. / Goldstein, B.M. / Klinman, J.P. / Bahnson, B.J. #1: Journal: Eur.J.Biochem. / Year: 1994 Title: A few amino acid substitutions are responsible for the higher thermostability of a novel NAD(+)-dependent bacillar alcohol dehydrogenase Authors: Cannio, R. / Rossi, M. / Bartolucci, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rjw.cif.gz | 267.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rjw.ent.gz | 216.4 KB | Display | PDB format |
PDBx/mmJSON format | 1rjw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rj/1rjw ftp://data.pdbj.org/pub/pdb/validation_reports/rj/1rjw | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 36384.160 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Strain: LLD-R / Gene: ADH-HT / Plasmid: PRC17 / Production host: Escherichia coli (E. coli) / Strain (production host): RB791 / References: UniProt: P42328, alcohol dehydrogenase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-ETF / #4: 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: 2.51 Å3/Da / Density % sol: 50.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20MG/ML PROTEIN, 100MM HEPES, 12% TRIFLUOROETHANOL, 12% PEG 4000, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908 / Wavelength: 0.908 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→41.44 Å / Num. all: 55369 / Num. obs: 55369 / % possible obs: 87.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.769 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.35→2.37 Å / Redundancy: 4.696 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 6.3 / % possible all: 90.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: E. COLI NAD(+)-DEPENDENT TETRAMERIC ALCOHOL DEHYDROGENASE Resolution: 2.35→41.44 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 398738.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: RESTRAINTS FOR 222 NON-CRYSTALLOGRAPHIC SYMMETRY WERE APPLIED TO 2238 OF 2554 ATOMS IN EACH PROTEIN SUBUNIT.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.6042 Å2 / ksol: 0.353307 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→41.44 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINED / Rms dev Biso : 1.718 Å2 / Rms dev position: 0.107 Å / Weight Biso : 2 / Weight position: 50 | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.35→2.49 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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