[English] 日本語
Yorodumi- PDB-1dak: DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX REACTION I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dak | ||||||
---|---|---|---|---|---|---|---|
Title | DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX REACTION INTERMEDIATE ADP AND MIXED ANHYDRIDE | ||||||
Components | DETHIOBIOTIN SYNTHETASE | ||||||
Keywords | LIGASE / PHOSHPORYL TRANSFER / BIOTIN BIOSYNTHESIS / KINETIC CRYSTALLOGRAPHY | ||||||
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 / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 1.6 Å | ||||||
Authors | Kaeck, H. / Gibson, K.J. / Lindqvist, Y. / Schneider, G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: Snapshot of a phosphorylated substrate intermediate by kinetic crystallography. Authors: Kack, H. / Gibson, K.J. / Lindqvist, Y. / Schneider, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1dak.cif.gz | 62.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1dak.ent.gz | 44 KB | Display | PDB format |
PDBx/mmJSON format | 1dak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dak_validation.pdf.gz | 496.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1dak_full_validation.pdf.gz | 499.1 KB | Display | |
Data in XML | 1dak_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 1dak_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/1dak ftp://data.pdbj.org/pub/pdb/validation_reports/da/1dak | HTTPS FTP |
-Related structure data
Related structure data | 1a82C 1dahS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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) / Cellular location: CYTOPLASM / Cellular location (production host): CYTOPLASM / Gene (production host): BIOD / Production host: Escherichia coli (E. coli) / References: UniProt: P13000, dethiobiotin synthase |
---|
-Non-polymers , 5 types, 221 molecules
#2: Chemical | ChemComp-PO4 / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | ChemComp-DPU / | #5: Chemical | ChemComp-ADP / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.3 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 8.5 / Details: pH 8.5 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusionDetails: drop contained 0.003ml of protein solution mixed with 0.074ml of well solution. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 0.7606 |
Detector | Type: PRINCETON 2K / Detector: CCD / Date: Oct 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7606 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→25 Å / Num. obs: 86120 / % possible obs: 99 % / Redundancy: 3.2 % / Rsym value: 0.078 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.43 / % possible all: 92.4 |
Reflection | *PLUS Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS % possible obs: 92.4 % / Rmerge(I) obs: 0.43 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 1DAH, WITH NON-PROTEIN ATOMS EXCLUDED Resolution: 1.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.184 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |