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- PDB-2bfb: Reactivity modulation of human branched-chain alpha-ketoacid dehy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bfb | |||||||||
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Title | Reactivity modulation of human branched-chain alpha-ketoacid dehydrogenase by an internal molecular switch | |||||||||
![]() | (2-OXOISOVALERATE DEHYDROGENASE ...) x 2 | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Machius, M. / Wynn, R.M. / Chuang, J.L. / Tomchick, D.R. / Brautigam, C.A. / Chuang, D.T. | |||||||||
![]() | ![]() Title: A Versatile Conformational Switch Regulates Reactivity in Human Branched-Chain Alpha-Ketoacid Dehydrogenase. Authors: Machius, M. / Wynn, R.M. / Chuang, J.L. / Tomchick, D.R. / Brautigam, C.A. / Chuang, D.T. #1: ![]() Title: Crosstalk between Cofactor Binding and the Phosphorylation Loop Conformation in the Bckd Machine 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. / Machius, M. / Chuang, J. / Li, J. / Tomchick, D. / Chuang, D. #3: Journal: J.Biol.Chem. / Year: 2001 Title: Roles of Active Site and Novel K+ Ion-Binding Site Residues in Human Mitochondrial Branched-Chain Alpha-Ketoacid Decarboxylase/Dehydrogenase Authors: Wynn, R.M. / Ho, R. / Chuang, J.L. / Chuang, D.T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 177.8 KB | Display | ![]() |
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PDB format | ![]() | 138.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1wciC ![]() 2beuC ![]() 2bevC ![]() 2bewC ![]() 2bfcC ![]() 2bfdC ![]() 2bfeC ![]() 2bffC ![]() 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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Unit cell |
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Components on special symmetry positions |
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Components
-2-OXOISOVALERATE DEHYDROGENASE ... , 2 types, 2 molecules AB
#1: Protein | Mass: 45430.980 Da / Num. of mol.: 1 / Fragment: RESIDUES 46-445 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() Strain (production host): BL-21 CELLS WITH OVEREXPRESSING GROEL AND GROES 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 / Fragment: RESIDUES 51-392 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() Strain (production host): BL-21 CELLS WITH OVEREXPRESSING GROEL AND GROES References: UniProt: P21953, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) |
-Non-polymers , 7 types, 652 molecules ![](data/chem/img/K.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TPP.gif)
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![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/CL.gif)
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![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-MN / | #5: Chemical | ![]() #6: Chemical | ChemComp-TPP / | ![]() #7: Chemical | ChemComp-GOL / | ![]() #8: Chemical | ChemComp-MRD / ( | ![]() #9: Water | ChemComp-HOH / | ![]() |
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-Details
Compound details | ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 53.4 % |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion / pH: 5.5 Details: CRYSTALS WERE GROWN AT 22C VIA THE VAPOR DIFFUSION METHOD IN COMPLEX WITH A 40 AMINO ACID PEPTIDE DERIVED FROM THE SUBUNIT BINDING DOMAIN (SBD) OF THE E2 COMPONENT OF BRANCHED CHAIN ALPHA- ...Details: CRYSTALS WERE GROWN AT 22C VIA THE VAPOR DIFFUSION METHOD IN COMPLEX WITH A 40 AMINO ACID PEPTIDE DERIVED FROM THE SUBUNIT BINDING DOMAIN (SBD) OF THE E2 COMPONENT OF BRANCHED CHAIN ALPHA-KETOACID DEHDROGENASE. THIS COMPLEX WAS FORMED BY MIXING N-TERMINALLY HIS6-TAGGED PROTEIN WITH C-TERMINALLY HIS6-TAGGED SBD IN 50 MM NA-HEPES, PH 7.5, 150 MM KCL, 20 MM DTT AND 5% (V/V) GLYCEROL AT A MOLAR RATIO OF 1:4. CRYSTALS OF THE COMPLEX (20 MG/ML) WERE OBTAINED BY MIXING 3 MICROLITERS OF PROTEIN WITH 3 MICROLITERS OF CRYSTALLIZATION SOLUTION (10% (V/V) POLYETHYLENE GLYCOL 4000, 10% (V/V) MPD AND 0.1M SODIUM CITRATE, PH 5.8) WITH 1 ML OF CRYSTALLIZATION SOLUTION IN THE RESERVOIR. MANGANESE IONS WERE USED INSTEAD OF MAGNESIUM REQUIRED FOR THE BINDING OF THIAMIN DIPHOSPHATE TO THE ENZYME. THE PRESENCE OF MANGANESE IONS IN THE CRYSTALS RESULTED IN IMPROVED X-RAY DIFFRACTION QUALITIES WITHOUT AFFECTING THE CATALYTIC PROPERTIES. CRYSTALS WERE CRYO-PROTECTED BY STEP-WISE TRANSFER INTO CRYO-BUFFER (CRYSTALLIZATION SOLUTION CONTAINING 5-10%(V/V) GLYCEROL). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CUSTOM / Detector: CCD / Date: Apr 12, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.77→26.77 Å / Num. obs: 82758 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 18.88 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 1.77→1.8 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1OLS Resolution: 1.77→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.543 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY. THE SUBUNIT BINDING DOMAIN (SBD) USED IN THE CRYSTALLIZATION PROCEDURE WAS NOT INCLUDED ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY. THE SUBUNIT BINDING DOMAIN (SBD) USED IN THE CRYSTALLIZATION PROCEDURE WAS NOT INCLUDED IN THE MODEL, ALTHOUGH ELECTRON DENSITY FOR IT WAS PRESENT. THE SBD BINDS NEAR A CRYSTALLOGRAPHIC TWO-FOLD AXIS, LEADING TO OVERLAPPED AND AVERAGED ELECTRON DENSITY. THE QUALITY OF THE ELECTRON DENSITY DID NOT ALLOW UNAMBIGUOUS TRACING OF THIS PEPTIDE.
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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: 17.05 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→30 Å
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Refine LS restraints |
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