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Yorodumi- PDB-2eq9: Crystal structure of lipoamide dehydrogenase from thermus thermop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2eq9 | ||||||
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Title | Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with psbdb | ||||||
Components |
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Keywords | OXIDOREDUCTASE / PROTEIN-PROTEIN COMPLEX / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / acyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / glycolytic process / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Nakai, T. / Kamiya, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of lipoamide dehydrogenase from Thermus thermophilus HB8 Authors: Nakai, T. / Kamiya, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2eq9.cif.gz | 722.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eq9.ent.gz | 593.5 KB | Display | PDB format |
PDBx/mmJSON format | 2eq9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2eq9_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 2eq9_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 2eq9_validation.xml.gz | 145.2 KB | Display | |
Data in CIF | 2eq9_validation.cif.gz | 196.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/2eq9 ftp://data.pdbj.org/pub/pdb/validation_reports/eq/2eq9 | HTTPS FTP |
-Related structure data
Related structure data | 2eq6SC 2eq7C 2eq8C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 49151.836 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0233 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) / References: UniProt: Q5SLR0, dihydrolipoyl dehydrogenase #2: Protein/peptide | Mass: 4450.195 Da / Num. of mol.: 4 / Fragment: Peripheral subunit binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0232 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) References: UniProt: Q5SLR1, dihydrolipoyllysine-residue (2-methylpropanoyl)transferase #3: Chemical | ChemComp-FAD / #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: 2.61 Å3/Da / Density % sol: 52.86 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30%(w/v) PEG MME 5000, 200mM ammonium sulfate, 100mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 8, 2006 |
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: 2.09→50 Å / Num. obs: 238181 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.09→2.16 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 1.7 / Num. unique all: 21564 / % possible all: 87.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2EQ6 Resolution: 2.09→43.62 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2304764.35 / 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: 45.6929 Å2 / ksol: 0.335389 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.09→43.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.09→2.22 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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