+Open data
-Basic information
Entry | Database: PDB / ID: 1gkx | |||||||||
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Title | Branched-chain alpha-ketoacid dehydrogenase kinase (BCK) | |||||||||
Components | [3-METHYL-2-OXOBUTANOATE DEHYDROGENASE [LIPOAMIDE]] KINASE | |||||||||
Keywords | TRANSFERASE / MITOCHONDRIAL PROTEIN KINASE / POTASSIUM | |||||||||
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 / L-leucine catabolic process / valine catabolic process / isoleucine catabolic process / : / pyruvate dehydrogenase (acetyl-transferring) kinase activity / branched-chain amino acid catabolic process / regulation of glucose metabolic process ...[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase / [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity / Branched-chain amino acid catabolism / L-leucine catabolic process / valine catabolic process / isoleucine catabolic process / : / pyruvate dehydrogenase (acetyl-transferring) kinase activity / branched-chain amino acid catabolic process / 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: 2.3 Å | |||||||||
Authors | Machius, M. / Chuang, J.L. / Wynn, R.M. / Tomchick, D.R. / Chuang, D.T. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: Structure of Rat Bckd Kinase: Nucleotide-Induced Domain Communication in a Mitochondrial Protein Kinase. Authors: Machius, M. / Chuang, J.L. / Wynn, R.M. / Tomchick, D.R. / 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 | 1gkx.cif.gz | 74.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gkx.ent.gz | 58.4 KB | Display | PDB format |
PDBx/mmJSON format | 1gkx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/1gkx ftp://data.pdbj.org/pub/pdb/validation_reports/gk/1gkx | HTTPS FTP |
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-Related 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: 44261.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: C-TERMINAL HIS6-TAG / Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PTRCKINASEHIS6/PGROESL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): CG-712 / References: UniProt: Q00972, EC: 2.7.1.115 | ||||
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#2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | Sequence details | CRYSTALLIZ | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 64 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: VAPOR DIFFUSION, 20C, EQUAL AMOUNTS OF BCK (20 MG/ML IN 50 MM HEPES, PH 7.5, 1 M SODIUM CHLORIDE, 250 MM POTASSIUM CHLORIDE, 300 MM ARGININE, 20 MM BETA- MERCAPTOETHANOL, 2 MM BENZAMIDINE, 2 ...Details: VAPOR DIFFUSION, 20C, EQUAL AMOUNTS OF BCK (20 MG/ML IN 50 MM HEPES, PH 7.5, 1 M SODIUM CHLORIDE, 250 MM POTASSIUM CHLORIDE, 300 MM ARGININE, 20 MM BETA- MERCAPTOETHANOL, 2 MM BENZAMIDINE, 2 MM MAGNESIUM CHLORIDE, 0.5 MM PMSF, 10% (W/V) GLYCEROL) AND RESERVOIR (8%(W/V) PEG-6000, 5% (V/V) ETHYLENE GLYCOL, 1 M NACL, 20 MM BETA-MERCAPTOETHANOL) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.12713 |
Detector | Type: SBC-CAT / Detector: CCD / Date: Jun 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12713 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→48.52 Å / Num. obs: 27710 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 65.8 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 29 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 1.8 / % possible all: 97.5 |
Reflection | *PLUS Highest resolution: 2.98 Å / Lowest resolution: 35.5 Å / % possible obs: 99.4 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.023 |
Reflection shell | *PLUS Highest resolution: 2.98 Å / Lowest resolution: 3.1 Å / % possible obs: 94.5 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.785 / Mean I/σ(I) obs: 2.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: BRANCHED-CHAIN ALPHA-KETOACID DEHYDROGENASE KINASE (BCK) COMPLEXED WITH ATP-GAMMA-S Resolution: 2.3→48.52 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 722618.84 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.1487 Å2 / ksol: 0.353714 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→48.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.98 Å / Lowest resolution: 35.5 Å / Num. reflection obs: 11149 / Num. reflection Rfree: 1542 / Rfactor obs: 0.243 / Rfactor Rfree: 0.272 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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