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- PDB-5b6h: Crystal structure of an APRT from Yersinia pseudotuberculosis in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5b6h | ||||||
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Title | Crystal structure of an APRT from Yersinia pseudotuberculosis in complex with AMP. | ||||||
![]() | Adenine phosphoribosyltransferase | ||||||
![]() | TRANSFERASE / adenine phosphoribosyltransferase | ||||||
Function / homology | ![]() adenine salvage / adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / AMP salvage / purine ribonucleoside salvage / cytosol Similarity search - Function | ||||||
Biological species | Yersinia pseudotuberculosis serotype I | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
Model details | STRUCTURAL GENOMICS | ||||||
![]() | Pavithra, G.C. / Ramagopal, U.A. | ||||||
![]() | ![]() Title: Crystal structure of an APRT from Yersinia pseudotuberculosis in complex with AMP. Authors: Pavithra, G.C. / Ramagopal, U.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.4 KB | Display | ![]() |
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PDB format | ![]() | 64.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 776.2 KB | Display | ![]() |
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Full document | ![]() | 776.1 KB | Display | |
Data in XML | ![]() | 9.6 KB | Display | |
Data in CIF | ![]() | 12.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4mb6S 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19589.320 Da / Num. of mol.: 1 / Fragment: UNP residues 7-187 Source method: isolated from a genetically manipulated source Details: AMP complex Source: (gene. exp.) ![]() Strain: IP32953 / Gene: apt, YPTB0991 / Plasmid: LIC-PET30A / Production host: ![]() ![]() References: UniProt: Q66DQ2, adenine phosphoribosyltransferase | ||||
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#2: Chemical | ChemComp-AMP / | ||||
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.4M sodium malonate pH 7.0 these crystals were moved condition containing 25% PEG3350, 0.1M Tris-Hcl pH 8.5, 0.2M Sodium Acetate and soaked with 5mM AMP |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 3, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→48.2 Å / Num. obs: 17719 / % possible obs: 99.3 % / Redundancy: 5.9 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.054 / Net I/av σ(I): 27.149 / Net I/σ(I): 12.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4MB6 Resolution: 1.9→48.2 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.718 / SU ML: 0.098 / SU R Cruickshank DPI: 0.1433 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.129 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 66.43 Å2 / Biso mean: 26.827 Å2 / Biso min: 12.53 Å2
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Refinement step | Cycle: final / Resolution: 1.9→48.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.901→1.95 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 21.7073 Å / Origin y: -0.734 Å / Origin z: 7.1657 Å
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