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Yorodumi- PDB-3ak4: Crystal structure of NADH-dependent quinuclidinone reductase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ak4 | ||||||
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Title | Crystal structure of NADH-dependent quinuclidinone reductase from agrobacterium tumefaciens | ||||||
Components | NADH-dependent quinuclidinone reductase | ||||||
Keywords | OXIDOREDUCTASE / SDR / 3-QUINUCLIDINONE / (R)-3-QUINUCLIDINOL / CHIRAL ALCOHOL / CARBONYL REDUCTASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Agrobacterium tumefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Miyakawa, T. / Kataoka, M. / Takeshita, D. / Nomoto, F. / Nagata, K. / Shimizu, S. / Tanokura, M. | ||||||
Citation | Journal: To be Published Title: Crystal structure of NADH-dependent quinuclidinone reductase from Agrobacterium tumefaciens Authors: Miyakawa, T. / Kataoka, M. / Takeshita, D. / Nomoto, F. / Nagata, K. / Shimizu, S. / Tanokura, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ak4.cif.gz | 216.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ak4.ent.gz | 173.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ak4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/3ak4 ftp://data.pdbj.org/pub/pdb/validation_reports/ak/3ak4 | HTTPS FTP |
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-Related structure data
Related structure data | 1gegS 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
#1: Protein | Mass: 27588.557 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA(DE3) / References: UniProt: G1K3P5*PLUS #2: Chemical | ChemComp-NAD / #3: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THREE N-TERMINAL ...THE SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THREE N-TERMINAL RESIDUES ARE EXPRESSION | |
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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: 2.11 Å3/Da / Density % sol: 41.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 24% PEG3350, 100MM HEPES, 200MM AMMONIUM ACETATE, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Aug 3, 2008 |
Radiation | Monochromator: CONFOCAL MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 61144 / % possible obs: 98.1 % / Redundancy: 3.5 % / Rsym value: 0.045 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 7.5 / Num. unique all: 26076 / Rsym value: 0.15 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GEG Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.289 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R Free: 0.15 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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