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- PDB-1dam: DETHIOBIOTIN SYNTHETASE COMPLEXED WITH DETHIOBIOTIN, ADP, INORGAN... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1dam | ||||||||||||||||||||||||||||||||||||||||||
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Title | DETHIOBIOTIN SYNTHETASE COMPLEXED WITH DETHIOBIOTIN, ADP, INORGANIC PHOSPHATE AND MAGNESIUM | ||||||||||||||||||||||||||||||||||||||||||
![]() | PROTEIN (DETHIOBIOTIN SYNTHETASE) | ||||||||||||||||||||||||||||||||||||||||||
![]() | ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||
Function / homology | Dethiobiotin synthase BioD / P-loop containing nucleoside triphosphate hydrolase / CobQ/CobB/MinD/ParA nucleotide binding domain / ![]() ![]() ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||
Specimen source | ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||
Method | ![]() | ||||||||||||||||||||||||||||||||||||||||||
![]() | Kaeck, H. / Sandmark, J. / Gibson, K.J. / Schneider, G. / Lindqvist, Y. | ||||||||||||||||||||||||||||||||||||||||||
![]() | Journal: Protein Sci. / Year: 1998 Title: Crystal structure of two quaternary complexes of dethiobiotin synthetase, enzyme-MgADP-AlF3-diaminopelargonic acid and enzyme-MgADP-dethiobiotin-phosphate; implications for catalysis. ![]() #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: Snapshot of a Phosphorylated Substrate Intermediate by Kinetic Crystallography ![]() #2: Journal: Structure / Year: 1994 Title: Crystal Structure of an ATP-Dependent Carboxylase, Dethiobiotin Synthetase, at 1.65 A Resolution ![]() | ||||||||||||||||||||||||||||||||||||||||||
Validation Report | ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||
Date | Deposition: Aug 31, 1998 / Release: Jan 13, 1999
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmcif format | ![]() ![]() |
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PDB format | ![]() ![]() |
PDBML Plus | ![]() |
Others | ![]() |
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Links
-Related structure data
Related structure data | ![]() C1bs1 C: citing same article |
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Similar-shape strucutres |
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell | γ α β
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Components
-Protein/peptide , 1 types, 1 molecules A
#1: Protein/peptide | Mass: 24028.289 Da / Num. of mol.: 1 / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 204 molecules 








#2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Chemical | ChemComp-ADP / | #5: Chemical | ChemComp-DTB / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 / Density percent sol: 34 % | ||||||||||||||||||||||||||||||
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Crystal grow![]() | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temp: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 kelvins |
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Source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Collection date: Jul 1, 1996 |
Radiation | Monochromator: GRAPHITE / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | D resolution high: 1.8 Å / D resolution low: 3 Å / Number obs: 17046 / Rsym value: 0.044 / NetI over sigmaI: 18.1 / Redundancy: 2.5 % / Percent possible obs: 90.6 |
Reflection shell | Highest resolution: 1.8 Å / Lowest resolution: 1.86 Å / MeanI over sigI obs: 3.3 / Rsym value: 0.337 / Percent possible all: 86.1 |
Reflection | *PLUS Number measured all: 42816 / Rmerge I obs: 0.044 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Percent possible obs: 86.1 / Rmerge I obs: 0.337 |
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Processing
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Refine | Method to determine structure![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | B iso mean: 15.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Least-squares process | R factor R free![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine hist #LAST | Highest resolution: 1.8 Å / Lowest resolution: 2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Number of atoms included #LAST | Protein: 1692 / Nucleic acid: 0 / Ligand: 49 / Solvent: 199 / Total: 1940 | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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