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- PDB-5zmi: Crystal structure of APRT from Y. pseudotuberculosis in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zmi | ||||||
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Title | Crystal structure of APRT from Y. pseudotuberculosis in complex with adenine. | ||||||
![]() | Adenine phosphoribosyltransferase | ||||||
![]() | TRANSFERASE / adenine phosphoribosyltransferase / adenine | ||||||
Function / homology | ![]() adenine salvage / adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / AMP salvage / purine ribonucleoside salvage / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pavithra, G.C. / Fox, G.C. / Ramagopal, U.A. | ||||||
![]() | ![]() Title: Crystal structure of adenine phosphoribosyltransferase from Yersinia pseudotuberculosis 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 | ![]() | 83.6 KB | Display | ![]() |
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PDB format | ![]() | 61.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 742.8 KB | Display | ![]() |
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Full document | ![]() | 742.8 KB | Display | |
Data in XML | ![]() | 8.6 KB | Display | |
Data in CIF | ![]() | 10.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4mb6SC ![]() 5zc7C 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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Components
#1: Protein | Mass: 20165.990 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: IP32953 / Gene: YPTB0991 / Plasmid: pNIC28-Bsa4 / Production host: ![]() ![]() References: UniProt: Q66DQ2, adenine phosphoribosyltransferase |
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#2: Chemical | ChemComp-ADE / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.95 % / Mosaicity: 0.68 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30% PEG4000, 0.1M Tris-Hcl pH 8.5, 0.2M Sodium Acetate with 5mM adenine and 5% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→48.57 Å / Num. obs: 13665 / % possible obs: 98.1 % / Redundancy: 2.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.034 / Rrim(I) all: 0.061 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.05→2.11 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.49 / Num. unique obs: 1026 / CC1/2: 0.731 / Rpim(I) all: 0.375 / Rrim(I) all: 0.62 / % possible all: 94.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4MB6 Resolution: 2.05→48.57 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 11.233 / SU ML: 0.136 / SU R Cruickshank DPI: 0.1654 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.155 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: 102.09 Å2 / Biso mean: 58.491 Å2 / Biso min: 36.35 Å2
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Refinement step | Cycle: final / Resolution: 2.05→48.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 21.0714 Å / Origin y: -0.1791 Å / Origin z: 7.3287 Å
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