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Yorodumi- PDB-2eq6: Crystal structure of lipoamide dehydrogenase from thermus thermop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2eq6 | ||||||
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Title | Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 | ||||||
Components | Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component | ||||||
Keywords | OXIDOREDUCTASE / homodimer / 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 / glycolytic process / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 | 2eq6.cif.gz | 198.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eq6.ent.gz | 152.9 KB | Display | PDB format |
PDBx/mmJSON format | 2eq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/2eq6 ftp://data.pdbj.org/pub/pdb/validation_reports/eq/2eq6 | HTTPS FTP |
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-Related structure data
Related structure data | 2eq7C 2eq8C 2eq9C 1ebdS 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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Unit cell |
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-Components
#1: Protein | Mass: 49151.836 Da / Num. of mol.: 2 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: Chemical | #3: 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: 2.56 Å3/Da / Density % sol: 51.98 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 8%(w/v) PEG 6000, 6%(v/v) MPD, 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: BL44B2 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 11, 2001 |
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: 1.6→20 Å / Num. obs: 123505 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 1.98 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 1.6 / Num. unique all: 6807 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EBD Resolution: 1.6→19.81 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1041334.96 / 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: 60.7956 Å2 / ksol: 0.375703 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→19.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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