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Yorodumi- PDB-1zk2: Orthorhombic crystal structure of the apo-form of R-specific alco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zk2 | ||||||
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Title | Orthorhombic crystal structure of the apo-form of R-specific alcohol dehydrogenase (mutant G37D) from Lactobacillus brevis | ||||||
Components | R-specific alcohol dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / short chain reductases/dehydrogenases / magnesium dependence / R-specific alcohol dehydrogenase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Lactobacillus brevis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Schlieben, N.H. / Niefind, K. / Muller, J. / Riebel, B. / Hummel, W. / Schomburg, D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Atomic resolution structures of R-specific alcohol dehydrogenase from Lactobacillus brevis provide the structural bases of its substrate and cosubstrate specificity Authors: Schlieben, N.H. / Niefind, K. / Muller, J. / Riebel, B. / Hummel, W. / Schomburg, D. #1: Journal: J.Mol.Biol. / Year: 2003 Title: The crystal structure of R-specific alcohol dehydrogenase from Lactobacillus brevis suggests the structural basis of its metal dependency Authors: Niefind, K. / Muller, J. / Riebel, B. / Hummel, W. / Schomburg, D. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Crystallization and preliminary characterization of crystals of R-alcohol dehydrogenase from Lactobacills brevis Authors: Niefind, K. / Riebel, B. / Muller, J. / Hummel, W. / Schomburg, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zk2.cif.gz | 74.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zk2.ent.gz | 54.7 KB | Display | PDB format |
PDBx/mmJSON format | 1zk2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/1zk2 ftp://data.pdbj.org/pub/pdb/validation_reports/zk/1zk2 | HTTPS FTP |
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-Related structure data
Related structure data | 1zjyC 1zjzC 1zk0C 1zk1C 1zk3C 1zk4C 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 on special symmetry positions |
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Details | The biological assembly is a tetramer generated form the monomer in the asymmetric unit by the following operations: x, y, z; -x, -y, z; -x, y, -z; x, -y, -z |
-Components
#1: Protein | Mass: 26714.098 Da / Num. of mol.: 1 / Mutation: G37D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus brevis (bacteria) / Plasmid: pkk177-3H / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q84EX5, alcohol dehydrogenase (NADP+) |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 47.5 % |
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→65.3 Å / Num. all: 37100 / Num. obs: 36602 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→65.3 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.185 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.886 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→65.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20 /
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