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- PDB-1u5b: Crystal structure of the human mitochondrial branched-chain alpha... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1u5b | |||||||||
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Title | Crystal structure of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase | |||||||||
![]() | (2-oxoisovalerate dehydrogenase ...) x 2 | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wynn, R.M. / Kato, M. / Machius, M. / Chuang, J.L. / Li, J. / Tomchick, D.R. / Chuang, D.T. | |||||||||
![]() | ![]() Title: Molecular mechanism for regulation of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase complex by phosphorylation Authors: Wynn, R.M. / Kato, M. / Machius, M. / Chuang, J.L. / Li, J. / Tomchick, D.R. / Chuang, D.T. #1: ![]() Title: Crosstalk between thiamin diphosphate binding and phosphorylation loop conformation in human branched-chain A-ketoacid decarboxylase/dehydrogenase Authors: Li, J. / Wynn, R.M. / Machius, M. / Chuang, J.L. / KARTHIKEYAN, S. / Tomchick, D.R. / Chuang, D.T. #2: ![]() Title: Roles of His291-alpha and His146-beta in the reductive acylation reaction catalyzed by human branched-chain alpha-ketoacid dehydrogenase: refined phosphorylation loop structure in the active site Authors: Wynn, R.M. / Machius, M. / Chuang, J.L. / Li, J. / Tomchick, D.R. / Chuang, D.T. | |||||||||
History |
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Remark 400 | SBD MOLECULE DETAILS MOLECULE: DIHYDROLIPOYLLYSINE-RESIDUE (2-METHYLPROPANOYL) TRANSFERASE; ...SBD MOLECULE DETAILS MOLECULE: DIHYDROLIPOYLLYSINE-RESIDUE (2-METHYLPROPANOYL) TRANSFERASE; FRAGMENT: SUBUNIT-BINDING DOMAIN; EC: 2.3.1.168; GENE: BCATE2; THE SBD MOLECULE WAS CREATED FROM A GENETICALLY MODIFIED SOURCE CONSISTENT WITH THE THE SOURCE RECORDS OF THE ALPHA AND BETA SUBUNITS OF 2-OXOISOVALERATE DEHYDROGENASE FOUND IN THIS STRUCTURE. SEQUENCE: GEIKGRKTLATPAVRRLAMENNIKLSEVVGSGKDGRILKEDILNYLEKQTLEHHHHHH 1 58 RESIDUES 2-50 CORRESPOND TO RESIDUES 165-213 OF SWISSPROT ENTRY ODB2_HUMAN, ACCESSION NUMBER P11182. THE FIRST GLYCINE RESIDUE IS A CLONING ARTIFACT. THE LAST 8 C-TERMINAL RESIDUES (LEHHHHHH) ARE HIS TAG RESIDUES. | |||||||||
Remark 999 | SEQUENCE The subunit-binding domain (SBD) of the E2 protein binds to the C-terminal region of the ...SEQUENCE The subunit-binding domain (SBD) of the E2 protein binds to the C-terminal region of the E1 beta subunit. However, the electron density of this domain is too weak to build a model, therefore this molecule has not been modeled in the coordinates. Further information on this molecule can be found in Remark 400. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 174.2 KB | Display | ![]() |
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PDB format | ![]() | 133.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1x7wC ![]() 1x7xC ![]() 1x7yC ![]() 1x7zC ![]() 1x80C ![]() 1olsS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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 a heterotetramer generated from the heterodimer in the asymmetric unit by the operations: x, -y, 2/3-z. |
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Components
-2-oxoisovalerate 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.) ![]() ![]() ![]() ![]() ![]() 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.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P21953, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) |
-Non-polymers , 5 types, 484 molecules ![](data/chem/img/K.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/TPP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/TPP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-MN / | #5: Chemical | ChemComp-TPP / | ![]() #6: Chemical | ChemComp-GOL / | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: PEG4000, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 2002 | |||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.83→50 Å / Num. all: 71894 / Num. obs: 71894 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.106 / Net I/σ(I): 16.9 | |||||||||
Reflection shell | Resolution: 1.83→1.86 Å / Rmerge(I) obs: 0.889 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1OLS Resolution: 1.83→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.868 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.109 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 24.995 Å2
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Refinement step | Cycle: LAST / Resolution: 1.83→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.831→1.879 Å / Total num. of bins used: 20
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