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Yorodumi- PDB-1dae: DETHIOBIOTIN SYNTHETASE COMPLEXED WITH 3-(1-AMINOETHYL) NONANEDIO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dae | ||||||
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Title | DETHIOBIOTIN SYNTHETASE COMPLEXED WITH 3-(1-AMINOETHYL) NONANEDIOIC ACID | ||||||
Components | DETHIOBIOTIN SYNTHETASE | ||||||
Keywords | LIGASE / BIOTIN BIOSYNTHESIS / MAGNESIUM / ATP-BINDING | ||||||
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 / Resolution: 1.7 Å | ||||||
Authors | Huang, W. / Jia, J. / Schneider, G. / Lindqvist, Y. | ||||||
Citation | Journal: Biochemistry / Year: 1995 Title: Mechanism of an ATP-dependent carboxylase, dethiobiotin synthetase, based on crystallographic studies of complexes with substrates and a reaction intermediate. Authors: Huang, W. / Jia, J. / Gibson, K.J. / Taylor, W.S. / Rendina, A.R. / Schneider, G. / Lindqvist, Y. #1: 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 | 1dae.cif.gz | 57.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dae.ent.gz | 40.9 KB | Display | PDB format |
PDBx/mmJSON format | 1dae.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dae_validation.pdf.gz | 374.4 KB | Display | wwPDB validaton report |
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Full document | 1dae_full_validation.pdf.gz | 376.8 KB | Display | |
Data in XML | 1dae_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 1dae_validation.cif.gz | 9.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/1dae ftp://data.pdbj.org/pub/pdb/validation_reports/da/1dae | 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
#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) / Production host: Escherichia coli (E. coli) / References: UniProt: P13000, dethiobiotin synthase |
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#2: Chemical | ChemComp-IKT / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 34 % | |||||||||||||||||||||
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Crystal grow | *PLUS Method: other / Details: cocrystallization | |||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Mar 6, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 20347 / % possible obs: 88 % / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Rmerge(I) obs: 0.05 |
Reflection | *PLUS Highest resolution: 1.7 Å / Num. obs: 23576 / % possible obs: 95 % / Num. measured all: 60324 |
-Processing
Software |
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Refinement | Resolution: 1.7→6 Å / σ(F): 1 /
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Displacement parameters | Biso mean: 22.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.173 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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