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- PDB-5ubg: Catalytic core domain of Adenosine triphosphate phosphoribosyltra... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ubg | ||||||
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Title | Catalytic core domain of Adenosine triphosphate phosphoribosyltransferase from Campylobacter jejuni with bound Phosphoribosyl-ATP | ||||||
![]() | ATP phosphoribosyltransferase | ||||||
![]() | TRANSFERASE / Histidine-biosynthesis / HisG / PR-ATP | ||||||
Function / homology | ![]() ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / L-histidine biosynthetic process / amino acid 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 | ![]() | 202.2 KB | Display | ![]() |
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PDB format | ![]() | 159.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5ub9SC ![]() 5ubhC ![]() 5ubiC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 4 - 225 / Label seq-ID: 5 - 226
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Details | The authors state that the protein exists as dimer with a molecular mass of 50 kDa in solution as evidenced by SEC, AUC, and light scattering experiments |
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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 | ChemComp-ZN / #3: Chemical | #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: 2.43 Å3/Da / Density % sol: 50.46 % / Description: octahedral 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, formed crystals soaked with 5 mM PR-ATP for 30-60 min 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: Apr 2, 2014 |
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→34.55 Å / Num. obs: 40502 / % possible obs: 99.8 % / Redundancy: 10.8 % / CC1/2: 1 / Rmerge(I) obs: 0.067 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 3.2 / CC1/2: 0.769 / % possible all: 97.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: single chain of PDB 5UB9 Resolution: 1.9→34.55 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.913 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.029 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.602 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→34.55 Å
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Refine LS restraints |
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