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Yorodumi- PDB-2dsd: Crystal structure of human ADP-ribose pyrophosphatase NUDT5 in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dsd | ||||||
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Title | Crystal structure of human ADP-ribose pyrophosphatase NUDT5 in complex with magnesium and AMP | ||||||
Components | ADP-sugar pyrophosphatase | ||||||
Keywords | HYDROLASE / Nudix domain / ADPR / ADP-ribose pyrophosphatase / NUDT5 | ||||||
Function / homology | Function and homology information ADP-D-ribose pyrophosphorylase / ribonucleoside diphosphate catabolic process / ADP-sugar diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / ADP-ribose diphosphatase / nucleobase-containing small molecule metabolic process / 8-oxo-dGDP phosphatase / ADP-ribose diphosphatase activity / 8-oxo-GDP phosphatase activity ...ADP-D-ribose pyrophosphorylase / ribonucleoside diphosphate catabolic process / ADP-sugar diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / ADP-ribose diphosphatase / nucleobase-containing small molecule metabolic process / 8-oxo-dGDP phosphatase / ADP-ribose diphosphatase activity / 8-oxo-GDP phosphatase activity / D-ribose catabolic process / 8-oxo-dGDP phosphatase activity / Phosphate bond hydrolysis by NUDT proteins / ATP generation from poly-ADP-D-ribose / nucleotide metabolic process / snoRNA binding / nucleotidyltransferase activity / chromatin remodeling / magnesium ion binding / protein homodimerization activity / extracellular exosome / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Zha, M. / Zhong, C. / Ding, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Crystal Structures of Human NUDT5 Reveal Insights into the Structural Basis of the Substrate Specificity Authors: Zha, M. / Zhong, C. / Peng, Y. / Hu, H. / Ding, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dsd.cif.gz | 94.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dsd.ent.gz | 70.8 KB | Display | PDB format |
PDBx/mmJSON format | 2dsd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/2dsd ftp://data.pdbj.org/pub/pdb/validation_reports/ds/2dsd | HTTPS FTP |
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-Related structure data
Related structure data | 2dsbSC 2dscC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23393.389 Da / Num. of mol.: 2 / Fragment: residues 1-210 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT5 / Plasmid: pGEX4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q9UKK9, ADP-ribose diphosphatase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides #2: Chemical | ChemComp-MG / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 30% PEG 4000, 0.2M sodium acetate, 0.1M tris hydrochloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 4, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 12474 / Num. obs: 12038 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 52.9 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 2.6→2.69 Å / % possible all: 87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DSB Resolution: 2.6→37.01 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1134788.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: maximum likelihood
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.9045 Å2 / ksol: 0.322853 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→37.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
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Xplor file |
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