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- PDB-5ub9: Catalytic core domain of Adenosine triphosphate phosphoribosyltra... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ub9 | ||||||
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Title | Catalytic core domain of Adenosine triphosphate phosphoribosyltransferase from Campylobacter jejuni | ||||||
![]() | ATP phosphoribosyltransferase | ||||||
![]() | TRANSFERASE / Histidine-biosynthesis / HisG | ||||||
Function / homology | ![]() ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / L-histidine biosynthetic process / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mittelstaedt, G. / Jiao, W. / Livingstone, E.K. / Parker, E.J. | ||||||
![]() | ![]() Title: A dimeric catalytic core relates the short and long forms of ATP-phosphoribosyltransferase. Authors: Mittelstadt, G. / Jiao, W. / Livingstone, E.K. / Moggre, G.J. / Nazmi, A.R. / Parker, E.J. #1: ![]() Title: Campylobacter jejuni adenosine triphosphate phosphoribosyltransferase is an active hexamer that is allosterically controlled by the twisting of a regulatory tail. Authors: Mittelstaedt, G. / Moggre, G.J. / Panjikar, S. / Nazmi, A.R. / Parker, E.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 187.3 KB | Display | ![]() |
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PDB format | ![]() | 148.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.1 KB | Display | ![]() |
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Full document | ![]() | 455.2 KB | Display | |
Data in XML | ![]() | 21.1 KB | Display | |
Data in CIF | ![]() | 30.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ubgC ![]() 5ubhC ![]() 5ubiC ![]() 4yb5S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25340.268 Da / Num. of mol.: 2 / Fragment: residues 1-225 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: RM1221 / Gene: hisG, CJE1769 / Plasmid: pDEST15 / Details (production host): N-terminal GST tag / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.94 % / Description: octahedral crystal shape |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1 M sodium acetate pH 5.0, 0.01 M ZnCl2, 7-10% PEG 6000, crystals grow from precipitate PH range: 5 / Temp details: temperature controlled |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 6, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.959 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→39.96 Å / Num. obs: 38485 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 4.6 / CC1/2: 0.956 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: truncated chain of PDB 4YB5 Resolution: 1.9→39.96 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.277 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.031 / 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: 28.39 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→39.96 Å
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Refine LS restraints |
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