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Yorodumi- PDB-2eq8: Crystal structure of lipoamide dehydrogenase from thermus thermop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2eq8 | ||||||
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Title | Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with psbdp | ||||||
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 / dihydrolipoyllysine-residue acetyltransferase activity / pyruvate dehydrogenase complex / 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: 1.94 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 | 2eq8.cif.gz | 408.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eq8.ent.gz | 326.1 KB | Display | PDB format |
PDBx/mmJSON format | 2eq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2eq8_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 2eq8_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 2eq8_validation.xml.gz | 88.9 KB | Display | |
Data in CIF | 2eq8_validation.cif.gz | 131.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/2eq8 ftp://data.pdbj.org/pub/pdb/validation_reports/eq/2eq8 | HTTPS FTP |
-Related structure data
Related structure data | 2eq6SC 2eq7C 2eq9C 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 49151.836 Da / Num. of mol.: 4 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: 4292.950 Da / Num. of mol.: 2 / Fragment: Peripheral subunit binding domain / Source method: obtained synthetically Details: The 40-residue peptide corresponding to a domain of the TTHA0184 protein was synthesized by Greiner References: UniProt: Q5SLV9, dihydrolipoyllysine-residue acetyltransferase #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: 2.34 Å3/Da / Density % sol: 47.49 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 14%(w/v) PEG 3350, 100mM HEPES, pH 7.5, 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 RAXIS V / Detector: IMAGE PLATE / Date: Jun 28, 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: 1.94→50 Å / Num. obs: 139010 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 39.1 |
Reflection shell | Resolution: 1.94→2.01 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 10.2 / Num. unique all: 13440 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2EQ6 Resolution: 1.94→46.86 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2706511.34 / 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: 49.3615 Å2 / ksol: 0.301858 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.94→46.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→2.06 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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