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Yorodumi- PDB-3rwb: Crystal structure of complex of 4PAL (4-Pyridoxolactone) and PLDH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rwb | ||||||
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Title | Crystal structure of complex of 4PAL (4-Pyridoxolactone) and PLDH (tetrameric pyridoxal 4-dehydrogenase) from Mesorhizobium loti | ||||||
Components | Pyridoxal 4-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / SHORT CHAIN DEHYDROGENASE/REDUCTASE / PYRIDOXAL / 4-PYRIDOXOLACTONE / NAD+ | ||||||
Function / homology | Function and homology information pyridoxal 4-dehydrogenase / pyridoxal 4-dehydrogenase activity / vitamin B6 catabolic process Similarity search - Function | ||||||
Biological species | Mesorhizobium loti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.699 Å | ||||||
Authors | Chu, H.N. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of complex of 4PAL (4-Pyridoxolactone) and PLDH (tetrameric pyridoxal 4-dehydrogenase) from Mesorhizobium loti Authors: Yagi, T. / Chu, H.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rwb.cif.gz | 217.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rwb.ent.gz | 175.2 KB | Display | PDB format |
PDBx/mmJSON format | 3rwb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rwb_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 3rwb_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 3rwb_validation.xml.gz | 49.2 KB | Display | |
Data in CIF | 3rwb_validation.cif.gz | 70.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/3rwb ftp://data.pdbj.org/pub/pdb/validation_reports/rw/3rwb | HTTPS FTP |
-Related structure data
Related structure data | 3nugS 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: 25426.914 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mesorhizobium loti (bacteria) / Gene: mlr6807, pldh-t / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q988B7, pyridoxal 4-dehydrogenase #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-4PL / #4: Chemical | ChemComp-GOL / #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: 1.99 Å3/Da / Density % sol: 38.2 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M Sodium acetate, 0.1M Tris-HCl, PEG 4000 30%, 0.65mM Pyridoxal, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 9, 2010 |
Radiation | Monochromator: DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.699→39.066 Å / Num. obs: 88415 / Redundancy: 4.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NUG Resolution: 1.699→39 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.163 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.699→39 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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