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- PDB-1dxl: Dihydrolipoamide dehydrogenase of glycine decarboxylase from Pisu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1dxl | ||||||
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Title | Dihydrolipoamide dehydrogenase of glycine decarboxylase from Pisum Sativum | ||||||
![]() | DIHYDROLIPOAMIDE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / DIHYDROLIPOAMIDE DEHYDROGENASE / MULTIENZYME COMPLEX PROTEIN / PYRUVATE DEHYDROGENASE COMPLEX / GLYCINE DECARBOXYLASE COMPLEX / FLAVOPROTEIN | ||||||
Function / homology | ![]() glycine cleavage complex / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / cell redox homeostasis / flavin adenine dinucleotide binding / mitochondrial matrix / mitochondrion Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Faure, M. / Cohen-Addad, C. / Bourguignon, J. / Macherel, D. / Neuburger, M. / Douce, R. | ||||||
![]() | ![]() Title: Interaction between the Lipoamide-Containing H-Protein and the Lipoamide Dehydrogenase (L-Protein) of the Glycine Decarboxylase Multienzyme System. 2. Crystal Structure of H- and L-Proteins Authors: Faure, M. / Bourguignon, J. / Neuburger, M. / Macherel, D. / Sieker, L. / Ober, R. / Kahn, R. / Cohen-Addad, C. / Douce, R. #1: Journal: Biochem.J. / Year: 1996 Title: Glycine Decarboxylase and Pyruvate Dehydrogenase Complexes Share the Same Dihydrolipoamide Dehydrogenase in Pea Leaf Mitochondria: Evidence from Mass Spectrometry and Primary-Structure Analysis Authors: Bourguignon, J. / Merand, V. / Rawsthorne, S. / Forest, E. / Douce, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 332.4 KB | Display | ![]() |
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PDB format | ![]() | 273.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 689.9 KB | Display | ![]() |
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Full document | ![]() | 827.5 KB | Display | |
Data in XML | ![]() | 57.7 KB | Display | |
Data in CIF | ![]() | 81.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1dxmC ![]() 3ladS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | BIOLOGICAL_UNIT: HOMODIMERTHE ASYMETRIC UNIT CONTAINS 2 DIMERS (AB AND CD) |
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Components
#1: Protein | Mass: 49808.961 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-FAD / #3: Water | ChemComp-HOH / | Sequence details | THE SWISSPROT ENTRY P31023 GIVES THE SEQUENCE FROM BOURGUIGNON J., MACHEREL D., NEUBURGER M., DOUCE ...THE SWISSPROT ENTRY P31023 GIVES THE SEQUENCE FROM BOURGUIGNO | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 45 % | |||||||||||||||||||||||||
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Crystal grow | pH: 5 Details: 15 % PEG MME 5K, 100 MM MES PH 5, 0.45 % HEPTYL-B-D-THIOGLUCOPYRANOSIDE, 2MM POTASSIUM LIPOATE. | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 15, 1998 / Details: MULTILAYER MIRRORS |
Radiation | Monochromator: DIAMOND C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9475 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→30 Å / Num. obs: 33527 / % possible obs: 87 % / Redundancy: 3.4 % / Biso Wilson estimate: 87.2 Å2 / Rsym value: 0.063 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 3.15→3.32 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.254 / % possible all: 77.3 |
Reflection | *PLUS % possible obs: 86.7 % / Rmerge(I) obs: 0.063 |
Reflection shell | *PLUS % possible obs: 77.3 % / Rmerge(I) obs: 0.254 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3LAD Resolution: 3.15→15 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1953239.04 / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54 Å2 / ksol: 0.225025 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.15→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.15→3.35 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.325 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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