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Yorodumi- PDB-5qto: PanDDA analysis group deposition -- Crystal Structure of NUDT5 in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5qto | ||||||
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Title | PanDDA analysis group deposition -- Crystal Structure of NUDT5 in complex with 1R-0641 | ||||||
Components | ADP-sugar pyrophosphatase | ||||||
Keywords | HYDROLASE / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer | ||||||
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 / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.67 Å | ||||||
Authors | Dubianok, Y. / Krojer, T. / Kovacs, H. / Moriaud, F. / Wright, N. / Strain-Damerell, C. / Burgess-Brown, N. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / von Delft, F. | ||||||
Citation | Journal: To Be Published Title: PanDDA analysis group deposition Authors: Dubianok, Y. / Krojer, T. / Kovacs, H. / Moriaud, F. / Wright, N. / Strain-Damerell, C. / Burgess-Brown, N. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / von Delft, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5qto.cif.gz | 167.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5qto.ent.gz | 131.1 KB | Display | PDB format |
PDBx/mmJSON format | 5qto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5qto_validation.pdf.gz | 487.8 KB | Display | wwPDB validaton report |
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Full document | 5qto_full_validation.pdf.gz | 503.3 KB | Display | |
Data in XML | 5qto_validation.xml.gz | 33.8 KB | Display | |
Data in CIF | 5qto_validation.cif.gz | 45.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/5qto ftp://data.pdbj.org/pub/pdb/validation_reports/qt/5qto | HTTPS FTP |
-Group deposition
ID | G_1002105 (8 entries) |
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Title | PanDDA analysis group deposition |
Type | changed state |
Description | NUDIX domain of human NUDT5 screened against the BIONET Flourine Fragment Library by NMR and validated by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1 |
-Related structure data
Related structure data | 6gruS S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data set type: other data / Details: Complete PanDDA analysis |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#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 |
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-Non-polymers , 5 types, 274 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-PWG / #5: Chemical | ChemComp-EDO / #6: 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: 2.41 Å3/Da / Density % sol: 48.96 % / Mosaicity: 0.15 ° |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 33% PEG4000, 0.2 magnesium chloride, 0.1 M Tris |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.67→41.48 Å / Num. obs: 95026 / % possible obs: 94.2 % / Redundancy: 1.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.033 / Rrim(I) all: 0.047 / Net I/σ(I): 9.5 / Num. measured all: 166019 / Scaling rejects: 0 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 6GRU Resolution: 1.67→41.52 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.302 / SU ML: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 99.2 Å2 / Biso mean: 38.281 Å2 / Biso min: 16.93 Å2
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Refinement step | Cycle: final / Resolution: 1.67→41.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.667→1.71 Å / Total num. of bins used: 20
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