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Open data
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Basic information
Entry | Database: PDB / ID: 3emv | ||||||
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Title | Crystal structure of Plasmodium vivax PNP with sulphate | ||||||
![]() | Uridine phosphorylase, putative | ||||||
![]() | TRANSFERASE / BINARY COMPLEX / PURINE NUCLEOSIDE PHOSPHORYLASE / URIDINE PHOSPHORYLASE / PUTATIVE | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chaikuad, A. / Brady, R.L. | ||||||
![]() | ![]() Title: Conservation of structure and activity in Plasmodium purine nucleoside phosphorylases Authors: Chaikuad, A. / Brady, R.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.1 KB | Display | ![]() |
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PDB format | ![]() | 46.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.5 KB | Display | ![]() |
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Full document | ![]() | 444.7 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 15.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3enzC ![]() 2b94S C: citing same article ( 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 on special symmetry positions |
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Components
#1: Protein | Mass: 28326.807 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The sequence was initially assigned as uridine phosphorylase (in genome database) homologue, but now it is widely considered to be purine nucleoside phosphorylase. Therefore, this protein ...Details: The sequence was initially assigned as uridine phosphorylase (in genome database) homologue, but now it is widely considered to be purine nucleoside phosphorylase. Therefore, this protein should be under 2.4.2.1 not 2.4.2.3 as in the database reference Source: (gene. exp.) ![]() ![]() Gene: PVX_080575 / Plasmid: pET28a / Production host: ![]() ![]() References: UniProt: A5K9M4, purine-nucleoside phosphorylase |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.47 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 18% PEG 4000, 0.2M LiSO4, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 24, 2007 |
Radiation | Monochromator: double crystal Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0745 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→67.88 Å / Num. all: 14619 / Num. obs: 14619 / % possible obs: 80.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 4.3 / Num. measured obs: 875 / Rsym value: 0.234 / % possible all: 49 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2B94 Resolution: 1.85→33.98 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.899 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.213 / ESU R Free: 0.174 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.307 Å2
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Refine analyze | Luzzati coordinate error obs: 0.196 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→33.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.847→1.895 Å / Total num. of bins used: 20
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