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- PDB-5qh3: PanDDA analysis group deposition of models with modelled events (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5qh3 | ||||||
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Title | PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with NUOOA000191 | ||||||
![]() | Peroxisomal coenzyme A diphosphatase NUDT7 | ||||||
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Function / homology | ![]() butyryl-CoA catabolic process / propionyl-CoA metabolic process / propionyl-CoA catabolic process / malonyl-CoA catabolic process / Peroxisomal lipid metabolism / coenzyme A diphosphatase activity / medium-chain fatty-acyl-CoA catabolic process / coenzyme A catabolic process / acetyl-CoA catabolic process / succinyl-CoA catabolic process ...butyryl-CoA catabolic process / propionyl-CoA metabolic process / propionyl-CoA catabolic process / malonyl-CoA catabolic process / Peroxisomal lipid metabolism / coenzyme A diphosphatase activity / medium-chain fatty-acyl-CoA catabolic process / coenzyme A catabolic process / acetyl-CoA catabolic process / succinyl-CoA catabolic process / nucleoside diphosphate metabolic process / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Krojer, T. / Talon, R. / Fairhead, M. / Diaz Saez, L. / Bradley, A.R. / Aimon, A. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Ruda, G.F. ...Krojer, T. / Talon, R. / Fairhead, M. / Diaz Saez, L. / Bradley, A.R. / Aimon, A. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Ruda, G.F. / Szommer, T. / Srikannathasan, V. / Elkins, J. / Spencer, J. / London, N. / Nelson, A. / Brennan, P.E. / Huber, K. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / von Delft, F. | ||||||
![]() | ![]() Title: PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) Authors: Krojer, T. / Talon, R. / Fairhead, M. / Diaz Saez, L. / Bradley, A.R. / Aimon, A. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Ruda, G.F. / Szommer, T. / Srikannathasan, V. / Elkins, ...Authors: Krojer, T. / Talon, R. / Fairhead, M. / Diaz Saez, L. / Bradley, A.R. / Aimon, A. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Ruda, G.F. / Szommer, T. / Srikannathasan, V. / Elkins, J. / Spencer, J. / London, N. / Nelson, A. / Brennan, P.E. / Huber, K. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / von Delft, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 58.4 KB | Display | ![]() |
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PDB format | ![]() | 40.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Group deposition
ID | G_1002045 (37 entries) |
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Title | PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) |
Type | changed state |
Description | human NUDT7 screened against the 3D-Fragment Consortium Library by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1 |
-Related structure data
Related structure data | ![]() 5t3pS S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22197.600 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P0C024, ![]() | ||||||
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#2: Chemical | ![]() #3: Chemical | ![]() #4: Chemical | #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.08 Å3/Da / Density % sol: 69.87 % / Mosaicity: 0.08 ° |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M bis-tris pH 5.5 -- 0.1M ammonium acetate -- 5%(w/v) PEG10K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→29.78 Å / Num. obs: 43384 / % possible obs: 99.8 % / Redundancy: 11.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.016 / Rrim(I) all: 0.054 / Net I/σ(I): 24.8 / Num. measured all: 486478 / Scaling rejects: 0 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5T3P Resolution: 1.65→107.59 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.54 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.07 / 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: 108.38 Å2 / Biso mean: 32.894 Å2 / Biso min: 15.69 Å2
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Refinement step | Cycle: final / Resolution: 1.65→107.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.651→1.694 Å / Total num. of bins used: 20
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