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Yorodumi- PDB-1qs0: Crystal Structure of Pseudomonas Putida 2-oxoisovalerate Dehydrog... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qs0 | |||||||||
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Title | Crystal Structure of Pseudomonas Putida 2-oxoisovalerate Dehydrogenase (Branched-Chain Alpha-Keto Acid Dehydrogenase, E1B) | |||||||||
Components | (2-OXOISOVALERATE DEHYDROGENASE ...) x 2 | |||||||||
Keywords | OXIDOREDUCTASE / HETEROTETRAMER / THDP COFACTOR | |||||||||
Function / homology | Function and homology information 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) / 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity Similarity search - Function | |||||||||
Biological species | Pseudomonas putida (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å | |||||||||
Authors | Aevarsson, A. / Seger, K. / Turley, S. / Sokatch, J.R. / Hol, W.G.J. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: Crystal structure of 2-oxoisovalerate and dehydrogenase and the architecture of 2-oxo acid dehydrogenase multienzyme complexes. Authors: Aevarsson, A. / Seger, K. / Turley, S. / Sokatch, J.R. / 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 | 1qs0.cif.gz | 161.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qs0.ent.gz | 131.4 KB | Display | PDB format |
PDBx/mmJSON format | 1qs0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qs/1qs0 ftp://data.pdbj.org/pub/pdb/validation_reports/qs/1qs0 | HTTPS FTP |
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-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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-Components
-2-OXOISOVALERATE DEHYDROGENASE ... , 2 types, 2 molecules AB
#1: Protein | Mass: 45594.355 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Plasmid: PJRS174 (PKT230 DERIVATIVE) / Production host: Pseudomonas putida (bacteria) / References: UniProt: P09060 |
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#2: Protein | Mass: 37509.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Plasmid: PJRS174 (PKT230 DERIVATIVE) / Production host: Pseudomonas putida (bacteria) / References: UniProt: P09061 |
-Non-polymers , 4 types, 200 molecules
#3: Chemical | ChemComp-MG / |
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#4: Chemical | ChemComp-TPP / |
#5: Chemical | ChemComp-COI / |
#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: 2.94 Å3/Da / Density % sol: 58.2 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.2 Details: POTASSIUM PHOSPHATE, DTT, MAGNESIUM CHLORIDE, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.88561,0.97888,0.97894 | ||||||||||||
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 21, 1998 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→39 Å / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 16 | ||||||||||||
Reflection | *PLUS Num. obs: 56728 / Num. measured all: 407418 | ||||||||||||
Reflection shell | *PLUS % possible obs: 74 % / Rmerge(I) obs: 0.182 |
-Processing
Software |
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Refinement | Resolution: 2.4→40 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3891686.62 / 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: 38.01 Å2 / ksol: 0.346 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.021 / 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: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 33.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.349 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.3 |