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- PDB-5vlb: Crystal Structure of Medicago truncatula L-Histidinol Dehydrogena... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5vlb | ||||||
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Title | Crystal Structure of Medicago truncatula L-Histidinol Dehydrogenase in Complex with Imidazole | ||||||
![]() | Histidinol dehydrogenase, chloroplastic![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ruszkowski, M. / Dauter, Z. | ||||||
![]() | ![]() Title: Structures of Medicago truncatula L-Histidinol Dehydrogenase Show Rearrangements Required for NAD(+) Binding and the Cofactor Positioned to Accept a Hydride. Authors: Ruszkowski, M. / Dauter, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 974.9 KB | Display | ![]() |
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PDB format | ![]() | 813.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5vlcC ![]() 5vldC ![]() 1kaeS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 48193.730 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-IMD / ![]() #4: Chemical | ChemComp-PEG / ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.3 % |
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Crystal grow![]() | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Molecular Dimensions Morpheus Condition H1: 0.1 M Amino acids, 0.1 M Buffer System 1 pH 6.5, 50 % v/v Precipitant Mix 1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jun 12, 2015 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.25→38.52 Å / Num. obs: 120737 / % possible obs: 94.7 % / Redundancy: 5.15 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.25→2.39 Å / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 2.06 / Num. unique obs: 15117 / % possible all: 73.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1kae Resolution: 2.25→38.52 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 15.151 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.307 / ESU R Free: 0.223 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.071 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→38.52 Å
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Refine LS restraints |
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