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Yorodumi- PDB-3tz2: Crystal structure of branched-chain alpha-ketoacid dehydrogenase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tz2 | ||||||
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Title | Crystal structure of branched-chain alpha-ketoacid dehydrogenase kinase/phenylbutyrate complex | ||||||
Components | [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / GHKL protein kinase / Allosteric kinase inhibitor / Branched-chain alpha-ketoacid / Branched-chain amino acids / Maple syrup urine disease / Diabetes and obesity / Bergerat nucleotide-binding fold / Protein kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase / [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity / Branched-chain amino acid catabolism / : / valine catabolic process / isoleucine catabolic process / pyruvate dehydrogenase (acetyl-transferring) kinase activity / L-leucine catabolic process / branched-chain amino acid catabolic process / lipid biosynthetic process ...[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase / [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity / Branched-chain amino acid catabolism / : / valine catabolic process / isoleucine catabolic process / pyruvate dehydrogenase (acetyl-transferring) kinase activity / L-leucine catabolic process / branched-chain amino acid catabolic process / lipid biosynthetic process / protein serine/threonine phosphatase activity / regulation of glucose metabolic process / spermatogenesis / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / mitochondrion / ATP binding Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Tso, S.C. / Chuang, J.L. / Gui, W.J. / Wynn, R.M. / Li, J. / Chuang, D.T. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Structure-based design and mechanisms of allosteric inhibitors for mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase. Authors: Tso, S.C. / Qi, X. / Gui, W.J. / Chuang, J.L. / Morlock, L.K. / Wallace, A.L. / Ahmed, K. / Laxman, S. / Campeau, P.M. / Lee, B.H. / Hutson, S.M. / Tu, B.P. / Williams, N.S. / Tambar, U.K. / ...Authors: Tso, S.C. / Qi, X. / Gui, W.J. / Chuang, J.L. / Morlock, L.K. / Wallace, A.L. / Ahmed, K. / Laxman, S. / Campeau, P.M. / Lee, B.H. / Hutson, S.M. / Tu, B.P. / Williams, N.S. / Tambar, U.K. / Wynn, R.M. / Chuang, D.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tz2.cif.gz | 139.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tz2.ent.gz | 109.5 KB | Display | PDB format |
PDBx/mmJSON format | 3tz2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tz2_validation.pdf.gz | 443.6 KB | Display | wwPDB validaton report |
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Full document | 3tz2_full_validation.pdf.gz | 450.1 KB | Display | |
Data in XML | 3tz2_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 3tz2_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/3tz2 ftp://data.pdbj.org/pub/pdb/validation_reports/tz/3tz2 | HTTPS FTP |
-Related structure data
Related structure data | 3tz0C 3tz4C 3tz5C 4dzyC 4h7qC 4h81C 4h85C C: citing same article (ref.) |
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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: 47374.246 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Bckdk / Plasmid: pTrckHisB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21GroESL References: UniProt: Q00972, [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase |
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#2: Chemical | ChemComp-CLT / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.67 % |
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Crystal grow | Temperature: 289 K / pH: 7.5 Details: 14% peg8000, 0.1 M Tris, pH8.5, 1.2 M NaCl, 125mM KCl, 150mM Arg-HCl,20mM MgCl2, 5% glycerol , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2011 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→50 Å / Num. obs: 14403 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.061 / Rsym value: 0.044 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 2.85→2.9 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.903 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.751 / % possible all: 88.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→38.38 Å / SU ML: 0.66 / σ(F): 1.33 / Phase error: 27.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 83.51 Å2 / ksol: 0.36 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.85→38.38 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 3.3858 Å / Origin y: -30.5406 Å / Origin z: 10.5099 Å
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Refinement TLS group | Selection details: all |