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Yorodumi- PDB-5hn6: Crystal structure of beta-decarboxylating dehydrogenase (TK0280) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hn6 | ||||||
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Title | Crystal structure of beta-decarboxylating dehydrogenase (TK0280) from Thermococcus kodakarensis complexed with Mn and 3-isopropylmalate | ||||||
Components | Homoisocitrate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / homoisocitrate dehydrogenase / beta-decarboxylating dehydrogenase | ||||||
Function / homology | Function and homology information isocitrate dehydrogenase (NAD+) activity / 3-isopropylmalate dehydrogenase activity / isocitrate metabolic process / L-leucine biosynthetic process / tricarboxylic acid cycle / NAD binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | Thermococcus kodakarensis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Shimizu, T. / Tomita, T. / Nishiyama, M. | ||||||
Citation | Journal: Biochem. J. / Year: 2017 Title: Structure and function of an ancestral-type beta-decarboxylating dehydrogenase from Thermococcus kodakarensis Authors: Shimizu, T. / Yin, L. / Yoshida, A. / Yokooji, Y. / Hachisuka, S.I. / Sato, T. / Tomita, T. / Nishida, H. / Atomi, H. / Kuzuyama, T. / Nishiyama, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hn6.cif.gz | 79.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hn6.ent.gz | 57.7 KB | Display | PDB format |
PDBx/mmJSON format | 5hn6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hn/5hn6 ftp://data.pdbj.org/pub/pdb/validation_reports/hn/5hn6 | HTTPS FTP |
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-Related structure data
Related structure data | 5hn3C 5hn4SC 5hn5C 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38637.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea) Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK0280 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codonplus (RIL) / References: UniProt: Q5JFV8 |
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#2: Chemical | ChemComp-IPM / |
#3: Chemical | ChemComp-MN / |
#4: Chemical | ChemComp-MPD / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES, sodium chloride, 2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→142.89 Å / Num. obs: 16850 / % possible obs: 99.3 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 41.6 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HN4 Resolution: 2.5→142.89 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 8.757 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.342 / ESU R Free: 0.257 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.535 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→142.89 Å
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Refine LS restraints |
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