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Yorodumi- PDB-4yb5: Adenosine triphosphate phosphoribosyltransferase from Campylobact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yb5 | ||||||
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Title | Adenosine triphosphate phosphoribosyltransferase from Campylobacter jejuni in complex with the allosteric inhibitor histidine | ||||||
Components | ATP phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / Phosphoribosyltransferase / hexamer / Histidine complex | ||||||
Function / homology | Function and homology information ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / L-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: 2.24 Å | ||||||
Authors | Mittelstaedt, G. / Moggre, G.-J. / Parker, E.J. | ||||||
Citation | 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: Mittelstadt, 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 | 4yb5.cif.gz | 341.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yb5.ent.gz | 273.4 KB | Display | PDB format |
PDBx/mmJSON format | 4yb5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yb5_validation.pdf.gz | 502.3 KB | Display | wwPDB validaton report |
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Full document | 4yb5_full_validation.pdf.gz | 518.1 KB | Display | |
Data in XML | 4yb5_validation.xml.gz | 61.3 KB | Display | |
Data in CIF | 4yb5_validation.cif.gz | 82.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/4yb5 ftp://data.pdbj.org/pub/pdb/validation_reports/yb/4yb5 | HTTPS FTP |
-Related structure data
Related structure data | 4yb6C 4yb7C 1h3dS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 5 - 299 / Label seq-ID: 6 - 300
NCS ensembles :
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Details | Hexameric assembly in solution was confirmed by gel filtration, light scattering, analytic ultra centrifugation and SAXS experiments |
-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 33741.254 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (strain RM1221) (Campylobacter) Strain: RM1221 / Gene: hisG, CJE1769 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5HSJ4, ATP phosphoribosyltransferase |
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-Non-polymers , 6 types, 150 molecules
#2: Chemical | ChemComp-SCN / #3: Chemical | ChemComp-K / #4: Chemical | ChemComp-HIS / #5: Chemical | ChemComp-PGE / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.47 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Potassium Thiocyanate, BTP, PEG3350, histidine / Temp details: temperature controlled incubator |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.959 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.959 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→48.04 Å / Num. obs: 94235 / % possible obs: 99 % / Redundancy: 5 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 2 |
Reflection shell | Resolution: 2.24→2.28 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 2 / % possible all: 89.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H3D Resolution: 2.24→48.04 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.843 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.293 / ESU R Free: 0.212 / 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: 48.288 Å2
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Refinement step | Cycle: 1 / Resolution: 2.24→48.04 Å
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Refine LS restraints |
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