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Yorodumi- PDB-1dam: DETHIOBIOTIN SYNTHETASE COMPLEXED WITH DETHIOBIOTIN, ADP, INORGAN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dam | ||||||
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Title | DETHIOBIOTIN SYNTHETASE COMPLEXED WITH DETHIOBIOTIN, ADP, INORGANIC PHOSPHATE AND MAGNESIUM | ||||||
Components | PROTEIN (DETHIOBIOTIN SYNTHETASE) | ||||||
Keywords | LIGASE / BIOTIN BIOSYNTHESIS / MAGNESIUM / ATP-BINDING / PHOSPHORYL TRANSFER | ||||||
Function / homology | Function and homology information dethiobiotin synthase / dethiobiotin synthase activity / biotin biosynthetic process / magnesium ion binding / protein homodimerization activity / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 1.8 Å | ||||||
Authors | Kaeck, H. / Sandmark, J. / Gibson, K.J. / Schneider, G. / Lindqvist, Y. | ||||||
Citation | 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. Authors: Kack, H. / Sandmark, J. / Gibson, K.J. / Schneider, G. / Lindqvist, Y. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: Snapshot of a Phosphorylated Substrate Intermediate by Kinetic Crystallography Authors: Kaeck, H. / Gibson, K.J. / Schneider, G. / Lindqvist, Y. #2: Journal: Structure / Year: 1994 Title: Crystal Structure of an ATP-Dependent Carboxylase, Dethiobiotin Synthetase, at 1.65 A Resolution Authors: Huang, W. / Lindqvist, Y. / Schneider, G. / Gibson, K.J. / Flint, D. / Lorimer, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dam.cif.gz | 62.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dam.ent.gz | 44.1 KB | Display | PDB format |
PDBx/mmJSON format | 1dam.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dam_validation.pdf.gz | 806.1 KB | Display | wwPDB validaton report |
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Full document | 1dam_full_validation.pdf.gz | 808.3 KB | Display | |
Data in XML | 1dam_validation.xml.gz | 13 KB | Display | |
Data in CIF | 1dam_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/1dam ftp://data.pdbj.org/pub/pdb/validation_reports/da/1dam | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 24028.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene (production host): BIOD / Production host: Escherichia coli (E. coli) / References: UniProt: P13000, dethiobiotin synthase |
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 34 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jul 1, 1996 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 17046 / % possible obs: 90.6 % / Redundancy: 2.5 % / Rsym value: 0.044 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.8→1.86 Å / Mean I/σ(I) obs: 3.3 / Rsym value: 0.337 / % possible all: 86.1 |
Reflection | *PLUS Num. measured all: 42816 / Rmerge(I) obs: 0.044 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / % possible obs: 86.1 % / Rmerge(I) obs: 0.337 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 15.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / σ(F): 0 / % reflection Rfree: 4.7 % / Rfactor obs: 0.18 / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 15.6 Å2 |