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Open data
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Basic information
Entry | Database: PDB / ID: 4kxm | ||||||
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Title | Crystal structure of DNPH1 (RCL) WITH N6-ISOPENTENYL-AMP | ||||||
![]() | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 | ||||||
![]() | HYDROLASE / DEOXYRIBONUCLEOSIDE 5'-MONOPHOSPHATE N-GLYCOSIDASE | ||||||
Function / homology | ![]() Purine catabolism / deoxyribonucleoside 5'-monophosphate N-glycosidase activity / deoxyribonucleoside monophosphate catabolic process / nucleoside salvage / dGMP catabolic process / allantoin metabolic process / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / epithelial cell differentiation / positive regulation of cell growth / protein homodimerization activity ...Purine catabolism / deoxyribonucleoside 5'-monophosphate N-glycosidase activity / deoxyribonucleoside monophosphate catabolic process / nucleoside salvage / dGMP catabolic process / allantoin metabolic process / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / epithelial cell differentiation / positive regulation of cell growth / protein homodimerization activity / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Padilla, A. / Labesse, G. / Kaminski, P.A. | ||||||
![]() | ![]() Title: N (6)-substituted AMPs inhibit mammalian deoxynucleotide N-hydrolase DNPH1. Authors: Amiable, C. / Pochet, S. / Padilla, A. / Labesse, G. / Kaminski, P.A. #1: ![]() Title: Structure of the oncoprotein Rcl bound to three nucleotide analogues. Authors: Padilla, A. / Amiable, C. / Pochet, S. / Kaminski, P.A. / Labesse, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 230.3 KB | Display | ![]() |
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PDB format | ![]() | 184.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 23.6 KB | Display | |
Data in CIF | ![]() | 31.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4kxlC ![]() 4kxnC ![]() 4fyiS 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: 6IA / End label comp-ID: 6IA / Refine code: 6 / Auth seq-ID: 10 - 201 / Label seq-ID: 3
NCS ensembles :
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Components
#1: Protein | Mass: 17173.334 Da / Num. of mol.: 4 / Fragment: UNP residues 11-151 / Mutation: D69N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O35820, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds #2: Chemical | ChemComp-6IA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 18% PEG8K, 100 MM NaCaCo, 200 MM ZINC ACETATE, PH 6.5, vapor diffusion, hanging drop, temperature 291K |
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-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 18, 2010 |
Radiation | Monochromator: CHANNEL CUT ESRF MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979756 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→40.97 Å / Num. obs: 21068 / % possible obs: 92.04 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.24→2.39 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.107 / Mean I/σ(I) obs: 6.7 / % possible all: 65.4 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4FYI Resolution: 2.24→38.71 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.895 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 14.052 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.596 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 44.69 Å2 / Biso mean: 15.7391 Å2 / Biso min: 4.01 Å2
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Refinement step | Cycle: LAST / Resolution: 2.24→38.71 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.24→2.298 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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