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Yorodumi- PDB-5vlc: Crystal Structure of Medicago truncatula L-Histidinol Dehydrogena... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vlc | ||||||
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Title | Crystal Structure of Medicago truncatula L-Histidinol Dehydrogenase in Complex with L-Histidinol | ||||||
Components | Histidinol dehydrogenase, chloroplastic | ||||||
Keywords | OXIDOREDUCTASE / histidine biosynthesis / Zn2+ binding protein / NAD binding protein / plant protein | ||||||
Function / homology | Function and homology information histidinol dehydrogenase activity / L-histidine biosynthetic process / amino acid biosynthetic process / chloroplast / NAD binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Medicago truncatula (barrel medic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Ruszkowski, M. / Dauter, Z. | ||||||
Citation | Journal: Sci Rep / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vlc.cif.gz | 979.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vlc.ent.gz | 816.8 KB | Display | PDB format |
PDBx/mmJSON format | 5vlc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vlc_validation.pdf.gz | 491.1 KB | Display | wwPDB validaton report |
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Full document | 5vlc_full_validation.pdf.gz | 511.6 KB | Display | |
Data in XML | 5vlc_validation.xml.gz | 89.9 KB | Display | |
Data in CIF | 5vlc_validation.cif.gz | 126.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/5vlc ftp://data.pdbj.org/pub/pdb/validation_reports/vl/5vlc | HTTPS FTP |
-Related structure data
Related structure data | 5vlbC 5vldC 1kaeS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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.) Medicago truncatula (barrel medic) / Gene: MTR_2g030520 / Production host: Escherichia coli (E. coli) / Strain (production host): Gold / References: UniProt: G7IKX3, histidinol dehydrogenase #2: Chemical | ChemComp-HSO / #3: Chemical | ChemComp-ZN / #4: 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: 2.22 Å3/Da / Density % sol: 44.59 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: 100 mM MES pH 5.2, 200 mM NACl, 12% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97625 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Dec 17, 2016 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→48.73 Å / Num. obs: 175983 / % possible obs: 99.4 % / Redundancy: 6.14 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.97→2.09 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.905 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 27746 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1kae Resolution: 1.97→48.73 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 10.067 / SU ML: 0.133 / Cross valid method: FREE R-VALUE / ESU R: 0.165 / ESU R Free: 0.155 / 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: 47.206 Å2
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Refinement step | Cycle: 1 / Resolution: 1.97→48.73 Å
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