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Yorodumi- PDB-1nxq: Crystal Structure of R-alcohol dehydrogenase (RADH) (apoenyzme) f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nxq | ||||||
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Title | Crystal Structure of R-alcohol dehydrogenase (RADH) (apoenyzme) from Lactobacillus brevis | ||||||
Components | R-alcohol dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / short chain dehydrogenases/reductases / SDR enzyme family / Rossmann fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Lactobacillus brevis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | ||||||
Authors | Niefind, K. / Muller, J. / Riebel, B. / Hummel, W. / Schomburg, D. | ||||||
Citation | 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. #1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2000 Title: Crystallization and preliminary characterization of crystals of R-alcohol dehydrogenase from Lactobacillus 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 | 1nxq.cif.gz | 64.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nxq.ent.gz | 46.2 KB | Display | PDB format |
PDBx/mmJSON format | 1nxq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nxq_validation.pdf.gz | 417.3 KB | Display | wwPDB validaton report |
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Full document | 1nxq_full_validation.pdf.gz | 417.6 KB | Display | |
Data in XML | 1nxq_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 1nxq_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/1nxq ftp://data.pdbj.org/pub/pdb/validation_reports/nx/1nxq | HTTPS FTP |
-Related structure data
Related structure data | 2hsdS 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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Components on special symmetry positions |
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Details | The biological assembly is a tetramer generated from the monomer in the asymmetric unit by the following operations: x, -y, -z; -x, y, -z; -x, -y, z |
-Components
#1: Protein | Mass: 26656.061 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus brevis (bacteria) / Production host: Escherichia coli (E. coli) / 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: 2.39 Å3/Da / Density % sol: 48.18 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 40%(v/v) 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Niefind, K., (2000) Acta Crystallogr., D56, 1696. | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Nov 20, 1997 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→68.5 Å / Num. all: 26474 / Num. obs: 26183 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 14.5 Å2 / Rsym value: 0.059 / Net I/σ(I): 46.4 |
Reflection shell | Resolution: 1.79→1.86 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 11.2 / Rsym value: 0.235 / % possible all: 91.3 |
Reflection | *PLUS Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS % possible obs: 91.3 % / Rmerge(I) obs: 0.235 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB FILE 2HSD REDUCED TO A POLY-ALA CHAIN Resolution: 1.79→69.01 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.093 / 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: 17.002 Å2
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Refinement step | Cycle: LAST / Resolution: 1.79→69.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.794→1.84 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Lowest resolution: 68.5 Å / Rfactor Rfree: 0.178 / Rfactor Rwork: 0.15 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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