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Yorodumi- PDB-1um9: branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1um9 | ||||||
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Title | branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8 in apo-form | ||||||
Components |
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Keywords | OXIDOREDUCTASE / alpha(2)beta(2) tetramer / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) / 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity / metal ion binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Nakai, T. / Nakagawa, N. / Maoka, N. / Masui, R. / Kuramitsu, S. / Kamiya, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Ligand-induced Conformational Changes and a Reaction Intermediate in Branched-chain 2-Oxo Acid Dehydrogenase (E1) from Thermus thermophilus HB8, as Revealed by X-ray Crystallography Authors: Nakai, T. / Nakagawa, N. / Maoka, N. / Masui, R. / Kuramitsu, S. / Kamiya, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1um9.cif.gz | 273.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1um9.ent.gz | 219.2 KB | Display | PDB format |
PDBx/mmJSON format | 1um9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/1um9 ftp://data.pdbj.org/pub/pdb/validation_reports/um/1um9 | HTTPS FTP |
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-Related structure data
Related structure data | 1umbC 1umcC 1umdC 1dtwS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is an alpha(2)beta(2) tetramer in the asymmetric unit. |
-Components
#1: Protein | Mass: 41508.023 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pACYC184 / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) References: UniProt: P84129, UniProt: Q5SLR4*PLUS, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) #2: Protein | Mass: 35180.582 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) References: UniProt: P84130, UniProt: Q5SLR3*PLUS, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.72 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: lithium sulfate, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 27, 2002 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 108074 / Num. obs: 108074 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 1.9 / Num. unique all: 10605 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DTW Resolution: 2.2→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3993653.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.0172 Å2 / ksol: 0.375093 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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