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- PDB-2g09: X-ray structure of mouse pyrimidine 5'-nucleotidase type 1, produ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2g09 | ||||||
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Title | X-ray structure of mouse pyrimidine 5'-nucleotidase type 1, product complex | ||||||
![]() | Cytosolic 5'-nucleotidase III | ||||||
![]() | HYDROLASE / UniProt Q9D020 / UMPH-1 / Cytosolic 5'-nucleotidase III / Pyrimidine 5'-nucleotidase 1 / P5n-1 / NT5C3 PROTEIN / AAH38029 / BC038029 / MM.158936 / Lead Poisoning / STRUCTURAL GENOMICS FUNCTIONAL FOLLOW-UP STUDY / PROTEIN STRUCTURE INITIATIVE / PSI / CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS / CESG | ||||||
Function / homology | ![]() Pyrimidine catabolism / CMP catabolic process / dTMP catabolic process / UMP catabolic process / dCMP catabolic process / dUMP catabolic process / 7-methylguanosine nucleotidase / adenosine metabolic process / XMP 5'-nucleosidase activity / 5'-nucleotidase ...Pyrimidine catabolism / CMP catabolic process / dTMP catabolic process / UMP catabolic process / dCMP catabolic process / dUMP catabolic process / 7-methylguanosine nucleotidase / adenosine metabolic process / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / transferase activity / nuclear body / nucleotide binding / magnesium ion binding / endoplasmic reticulum / mitochondrion / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bitto, E. / Bingman, C.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG) | ||||||
![]() | ![]() Title: Structure of pyrimidine 5'-nucleotidase type 1. Insight into mechanism of action and inhibition during lead poisoning. Authors: Bitto, E. / Bingman, C.A. / Wesenberg, G.E. / McCoy, J.G. / Phillips, G.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 153.3 KB | Display | ![]() |
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PDB format | ![]() | 117.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 910.4 KB | Display | ![]() |
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Full document | ![]() | 915.7 KB | Display | |
Data in XML | ![]() | 32.3 KB | Display | |
Data in CIF | ![]() | 50 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bduSC ![]() 2g06C ![]() 2g07C ![]() 2g08C ![]() 2g0aC S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 2 / Auth seq-ID: 7 - 297 / Label seq-ID: 7 - 297
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Details | The biological unit is a monomer. There are 2 biological units in the asymmetric unit (chains A & B). |
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Components
#1: Protein | Mass: 34163.926 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.51 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.005 M BIS TRIS, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, PH 6.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (20-25% PEG 8K, 0.10 M ...Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.005 M BIS TRIS, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, PH 6.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (20-25% PEG 8K, 0.10 M PIPES PH 6.5) CRYSTALS SOAKED FOR 60 MINUTES IN WELL SOLUTION WITH 0.005 M magnesium chloride, 0.005 M UMP, temperature 277K, VAPOR DIFFUSION, HANGING DROP, pH 6.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2005 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97913 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 45396 / % possible obs: 98.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.11 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 3.42 / % possible all: 97.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BDU Resolution: 2.1→32.19 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 6.969 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.152 / 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.09 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→32.19 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.1→2.15 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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