+Open data
-Basic information
Entry | Database: PDB / ID: 1dtw | |||||||||
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Title | HUMAN BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE | |||||||||
Components | (BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE ...) x 2 | |||||||||
Keywords | OXIDOREDUCTASE / ThDP-binding fold / BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE | |||||||||
Function / homology | Function and homology information branched-chain alpha-ketoacid dehydrogenase complex / 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) / 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity / branched-chain amino acid catabolic process / oxoglutarate dehydrogenase complex / Branched-chain amino acid catabolism / carboxy-lyase activity / response to nutrient / response to glucocorticoid / response to cAMP ...branched-chain alpha-ketoacid dehydrogenase complex / 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) / 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity / branched-chain amino acid catabolic process / oxoglutarate dehydrogenase complex / Branched-chain amino acid catabolism / carboxy-lyase activity / response to nutrient / response to glucocorticoid / response to cAMP / lipid metabolic process / mitochondrial matrix / protein-containing complex binding / nucleolus / mitochondrion / nucleoplasm / metal ion binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å | |||||||||
Model details | THIS IS THE E1 COMPONENT OF AN ALPHA-KETOACID DEHYDROGENASE MULTIENZYME COMPLEX. A NUMBER OF ...THIS IS THE E1 COMPONENT OF AN ALPHA-KETOACID DEHYDROGENASE MULTIENZYME COMPLEX. A NUMBER OF MUTATIONS HAVE BEEN CHARACTERIZED IN THIS ENZYME THAT CAUSE MAPLE SYRUP URINE DISEASE. | |||||||||
Authors | AEvarsson, A. / Chuang, J.L. / Wynn, R.M. / Turley, S. / Chuang, D.T. / Hol, W.G.J. | |||||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: Crystal structure of human branched-chain alpha-ketoacid dehydrogenase and the molecular basis of multienzyme complex deficiency in maple syrup urine disease. Authors: AEvarsson, A. / Chuang, J.L. / Wynn, R.M. / Turley, S. / Chuang, D.T. / Hol, W.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dtw.cif.gz | 149.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dtw.ent.gz | 115.7 KB | Display | PDB format |
PDBx/mmJSON format | 1dtw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dtw_validation.pdf.gz | 454.3 KB | Display | wwPDB validaton report |
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Full document | 1dtw_full_validation.pdf.gz | 479.8 KB | Display | |
Data in XML | 1dtw_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 1dtw_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/1dtw ftp://data.pdbj.org/pub/pdb/validation_reports/dt/1dtw | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is alpha2beta2 heterotetramer with chains A and B forming one alpha subunit - the other alpha subunit symmetry partner is generated by a two-fold / The biological assembly is alpha2beta2 heterotetramer with chain C forming one beta subunit - the other beta subunit symmetry partner is generated by a two-fold |
-Components
-BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE ... , 2 types, 2 molecules AB
#1: Protein | Mass: 45571.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: P-HE1-HIS6 / Production host: Escherichia coli (E. coli) References: UniProt: P12694, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) |
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#2: Protein | Mass: 37902.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: P-HE1-HIS6 / Production host: Escherichia coli (E. coli) References: UniProt: P21953, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) |
-Non-polymers , 4 types, 52 molecules
#3: Chemical | ChemComp-MG / | ||||
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#4: Chemical | #5: Chemical | ChemComp-TPP / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.21 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Ethanol, PEG 8000,MES, potassium chloride, magnesium chloride, glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 20K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |
Detector | Detector: CCD / Date: 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 22910 / % possible obs: 99.9 % / Redundancy: 13.4 % / Biso Wilson estimate: 49.1 Å2 / Rmerge(I) obs: 0.14 |
Reflection | *PLUS Num. obs: 22910 / Num. measured all: 306699 |
-Processing
Software |
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Refinement | Resolution: 2.7→50 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2036465.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.33 Å2 / ksol: 0.361 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 4.9 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 36.1 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.375 / % reflection Rfree: 4.4 % / Rfactor Rwork: 0.304 |