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- PDB-2tmd: CORRELATION OF X-RAY DEDUCED AND EXPERIMENTAL AMINO ACID SEQUENCE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2tmd | ||||||
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Title | CORRELATION OF X-RAY DEDUCED AND EXPERIMENTAL AMINO ACID SEQUENCES OF TRIMETHYLAMINE DEHYDROGENASE | ||||||
![]() | TRIMETHYLAMINE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE | ||||||
Function / homology | ![]() trimethylamine dehydrogenase / trimethylamine dehydrogenase activity / fatty acid beta-oxidation, unsaturated, even number, reductase/isomerase pathway / 2,4-dienoyl-CoA reductase (NADPH) activity / FMN binding / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Mathews, F.S. / Lim, L.W. / White, S. | ||||||
![]() | ![]() Title: Correlation of x-ray deduced and experimental amino acid sequences of trimethylamine dehydrogenase. Authors: Barber, M.J. / Neame, P.J. / Lim, L.W. / White, S. / Matthews, F.S. #1: ![]() Title: Studies of Crystalline Trimethylamine Dehydrogenase in Three Oxidation States and in the Presence of Substrate and Inhibitor Authors: Bellamy, H.D. / Lim, L.W. / Mathews, F.S. / Dunham, W.R. #2: ![]() Title: Identification of Adp in the Iron-Sulfur Flavoprotein Trimethylamine Dehydrogenase Authors: Lim, L.W. / Mathews, F.S. / Steenkamp, D.J. #3: ![]() Title: Three-Dimensional Structure of the Iron-Sulfur Flavoprotein Trimethylamine Dehydrogenase at 2.4 Angstroms Resolution Authors: Lim, L.W. / Shamala, N. / Mathews, F.S. / Steenkamp, D.J. / Hamlin, R. / Xuong, N.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 305.9 KB | Display | ![]() |
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PDB format | ![]() | 245.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 662.3 KB | Display | ![]() |
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Full document | ![]() | 690.1 KB | Display | |
Data in XML | ![]() | 31.4 KB | Display | |
Data in CIF | ![]() | 49.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Atom site foot note | 1: THR A 70 - HIS A 71 OMEGA = 17.29 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: THR B 70 - HIS B 71 OMEGA = 16.18 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.971338, 0.217797, 0.095224), Vector: Details | THERE ARE TWO MOLECULES IN THE ASYMMETRIC UNIT. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. | |
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Components
#1: Protein | Mass: 81606.023 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: W3A1 / References: UniProt: P16099, EC: 1.5.99.7 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.51 % |
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Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, hanging dropDetails: taken from Lim, L. et al (1982). J. Mol. Biol., 162, 869-876., macro-seeding |
Components of the solutions | *PLUS Conc.: 10-12 % / Common name: PEG8000 |
-Data collection
Reflection | *PLUS Highest resolution: 2.4 Å / Num. obs: 133000 / Num. measured all: 430000 / Rmerge(I) obs: 0.032 |
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Processing
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Refinement | Resolution: 2.4→10 Å / Rfactor Rwork: 0.154 / Rfactor obs: 0.154 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 10 Å / Rfactor obs: 0.154 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 1.281 |