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- PDB-3qxc: Crystal structure of dethiobiotin synthetase (BioD) from Helicoba... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qxc | ||||||
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Title | Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with ATP | ||||||
![]() | Dethiobiotin synthetase | ||||||
![]() | LIGASE / DTBS / dethiobiotin synthetase / Structural Genomics / ATP binding / PSI-BIOLOGY / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | ![]() dethiobiotin synthase / dethiobiotin synthase activity / biotin biosynthetic process / magnesium ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Porebski, P.J. / Klimecka, M.M. / Chruszcz, M. / Murzyn, K. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: Structural characterization of Helicobacter pylori dethiobiotin synthetase reveals differences between family members. Authors: Porebski, P.J. / Klimecka, M. / Chruszcz, M. / Nicholls, R.A. / Murzyn, K. / Cuff, M.E. / Xu, X. / Cymborowski, M. / Murshudov, G.N. / Savchenko, A. / Edwards, A. / Minor, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119.7 KB | Display | ![]() |
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PDB format | ![]() | 90 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 806.9 KB | Display | ![]() |
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Full document | ![]() | 809.4 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 23.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2qmoSC ![]() 3mleC ![]() 3qxhC ![]() 3qxjC ![]() 3qxsC ![]() 3qxxC ![]() 3qy0C S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 27148.088 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 7 types, 345 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ATP / | ||||||
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#3: Chemical | ChemComp-MG / | ||||||
#4: Chemical | ChemComp-NO3 / | ||||||
#5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-GOL / | #7: Chemical | ChemComp-PEG / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20% PEG3350; 100 MM NH4NO3; 100 MM BIS-TRIS; 5% GLYCEROL; 10 MM 8-AMINOOCTANOIC ACID; SOAKED WITH 10 MM ATP, 10 MM MGCL2; IN SITU PROTEOLYSIS - CHYMOTRYPSIN, PH 5.5, VAPOR DIFFUSION, HANGING ...Details: 20% PEG3350; 100 MM NH4NO3; 100 MM BIS-TRIS; 5% GLYCEROL; 10 MM 8-AMINOOCTANOIC ACID; SOAKED WITH 10 MM ATP, 10 MM MGCL2; IN SITU PROTEOLYSIS - CHYMOTRYPSIN, PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SBC-3 / Detector: CCD / Date: Jul 12, 2008 / Details: MIRROR |
Radiation | Monochromator: SI-111 CHANNEL / Protocol: MOLECULAR REPLACEMENT / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→50 Å / Num. all: 45819 / Num. obs: 45819 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 35.1 |
Reflection shell | Resolution: 1.34→1.36 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1964 / Rsym value: 0.4 / % possible all: 83.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2QMO Resolution: 1.34→50 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.388 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.683 Å2
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Refinement step | Cycle: LAST / Resolution: 1.34→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.34→1.375 Å / Total num. of bins used: 20
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