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Yorodumi- PDB-5ubi: Catalytic core domain of Adenosine triphosphate phosphoribosyltra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ubi | ||||||
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Title | Catalytic core domain of Adenosine triphosphate phosphoribosyltransferase from Campylobacter jejuni with bound PRPP | ||||||
Components | ATP phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / Histidine-biosynthesis / HisG / PRPP | ||||||
Function / homology | Function and homology information ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / histidine biosynthetic process / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Campylobacter jejuni (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å | ||||||
Authors | Mittelstaedt, G. / Jiao, W. / Livingstone, E.K. / Parker, E.J. | ||||||
Citation | Journal: Biochem. J. / Year: 2018 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: Journal: Protein Sci. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ubi.cif.gz | 199.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ubi.ent.gz | 157.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ubi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/5ubi ftp://data.pdbj.org/pub/pdb/validation_reports/ub/5ubi | HTTPS FTP |
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-Related structure data
Related structure data | 5ub9SC 5ubgC 5ubhC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 0 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 0 / Auth seq-ID: 4 - 220 / Label seq-ID: 5 - 221
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Details | The authors state that the protein exists as dimer of 50 kDa in solution as evidenced by SEC, AUC, and light scattering experiments |
-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 25340.268 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (strain RM1221) (Campylobacter) Strain: RM1221 / Gene: hisG, CJE1769 / Plasmid: pDEST15 / Details (production host): N-terminal GST tag / Production host: Escherichia coli (E. coli) / Strain (production host): BL21*(DE3) / References: UniProt: Q5HSJ4, ATP phosphoribosyltransferase #4: Sugar | |
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-Non-polymers , 5 types, 220 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 47.97 % |
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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 were soaked with 3 mM PRPP 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: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.959 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: May 4, 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: 2.1→50 Å / Num. obs: 28897 / % possible obs: 99.9 % / Redundancy: 14.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Net I/σ(I): 27.3 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 3.7 / CC1/2: 0.896 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: single chain of 5UB9 Resolution: 2.14→45.56 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.913 / SU B: 12.324 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R Free: 0.049 / 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: 33.047 Å2
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Refinement step | Cycle: 1 / Resolution: 2.14→45.56 Å
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Refine LS restraints |
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