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Yorodumi- PDB-1dbs: MECHANISTIC IMPLICATIONS AND FAMILY RELATIONSHIPS FROM THE STRUCT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dbs | ||||||
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Title | MECHANISTIC IMPLICATIONS AND FAMILY RELATIONSHIPS FROM THE STRUCTURE OF DETHIOBIOTIN SYNTHETASE | ||||||
Components | DETHIOBIOTIN SYNTHETASE | ||||||
Keywords | BIOTIN BIOSYNTHESIS | ||||||
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: 1.8 Å | ||||||
Authors | Sawyer, L. / Alexeev, D. | ||||||
Citation | Journal: Structure / Year: 1994 Title: Mechanistic implications and family relationships from the structure of dethiobiotin synthetase. Authors: Alexeev, D. / Baxter, R.L. / Sawyer, L. #1: Journal: Structure / Year: 1994 Title: Crystal Structure of an ATP Dependent Carboxylase Dethiobiotin Synthetase at 1.65 Angstroms Resolution Authors: Huang, W. / Lundquist, Y. / Schneider, G. / Gibson, K.J. / Flint, D. / Lorimer, G. #2: Journal: J.Mol.Biol. / Year: 1994 Title: Sequence and Crystallization of Escherichia Coli Dethiobiotin Synthetase, the Penultimate Enzyme of Biotin Biosynthesis Authors: Alexeev, D. / Baxter, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dbs.cif.gz | 57.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dbs.ent.gz | 42.3 KB | Display | PDB format |
PDBx/mmJSON format | 1dbs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dbs_validation.pdf.gz | 373.2 KB | Display | wwPDB validaton report |
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Full document | 1dbs_full_validation.pdf.gz | 374.5 KB | Display | |
Data in XML | 1dbs_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 1dbs_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/1dbs ftp://data.pdbj.org/pub/pdb/validation_reports/db/1dbs | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: LOOP 209 - 212 HAS POOR ELECTRON DENSITY. / 2: HOH 403 MAY BE A SODIUM ION. |
-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) / References: UniProt: P13000, dethiobiotin synthase | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | HOH 403 MAY BE A SODIUM ION. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.68 % | |||||||||||||||||||||||||
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Crystal | *PLUS Density % sol: 33 % | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: microdialysis / pH: 6 | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | Resolution: 1.8→7 Å / Num. obs: 18656 / % possible obs: 98 % / Observed criterion σ(I): 3 |
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Reflection | *PLUS Rmerge(I) obs: 0.034 |
Reflection shell | *PLUS % possible obs: 92.3 % |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.179 / Rfactor obs: 0.179 / Highest resolution: 1.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.8 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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