+Open data
-Basic information
Entry | Database: PDB / ID: 6gru | ||||||
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Title | Crystal structure of human NUDT5 | ||||||
Components | ADP-sugar pyrophosphatase | ||||||
Keywords | HYDROLASE / Nudix domain / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information ADP-D-ribose pyrophosphorylase / ribonucleoside diphosphate catabolic process / ADP-ribose diphosphatase / nucleobase-containing small molecule metabolic process / 8-oxo-dGDP phosphatase / ADP-ribose diphosphatase activity / D-ribose catabolic process / ADP-sugar diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process ...ADP-D-ribose pyrophosphorylase / ribonucleoside diphosphate catabolic process / ADP-ribose diphosphatase / nucleobase-containing small molecule metabolic process / 8-oxo-dGDP phosphatase / ADP-ribose diphosphatase activity / D-ribose catabolic process / ADP-sugar diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / 8-oxo-GDP phosphatase activity / 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: 1.93 Å | ||||||
Authors | Dubianok, Y. / Collins, P. / Krojer, T. / Fairhead, M. / MacLean, E. / Diaz Saez, L. / Strain-Damerell, C. / Elkins, J. / Burgess-Brown, N. / Bountra, C. ...Dubianok, Y. / Collins, P. / Krojer, T. / Fairhead, M. / MacLean, E. / Diaz Saez, L. / Strain-Damerell, C. / Elkins, J. / Burgess-Brown, N. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Huber, K. / von Delft, F. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To Be Published Title: Crystal structure of human NUDT5 Authors: Dubianok, Y. / Elkins, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Huber, K. / von Delft, F. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gru.cif.gz | 163.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gru.ent.gz | 126.4 KB | Display | PDB format |
PDBx/mmJSON format | 6gru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gru_validation.pdf.gz | 478.8 KB | Display | wwPDB validaton report |
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Full document | 6gru_full_validation.pdf.gz | 491.8 KB | Display | |
Data in XML | 6gru_validation.xml.gz | 31 KB | Display | |
Data in CIF | 6gru_validation.cif.gz | 42.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/6gru ftp://data.pdbj.org/pub/pdb/validation_reports/gr/6gru | HTTPS FTP |
-Related structure data
Related structure data | 2dsdS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 23136.078 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT5, NUDIX5, HSPC115 / Production host: Escherichia coli (E. coli) References: UniProt: Q9UKK9, ADP-ribose diphosphatase, 8-oxo-dGDP phosphatase, ADP-D-ribose pyrophosphorylase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CL / | #4: Chemical | #5: 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: 2.6 Å3/Da / Density % sol: 52.68 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30% PEG4000, 0.2M magnesium chloride, 0.1M tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→43.49 Å / Num. obs: 64137 / % possible obs: 97.5 % / Redundancy: 2 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.93→1.98 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DSD Resolution: 1.93→32.03 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.624 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.167 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.909 Å2
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Refinement step | Cycle: 1 / Resolution: 1.93→32.03 Å
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Refine LS restraints |
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