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Yorodumi- PDB-5qh6: PanDDA analysis group deposition of models with modelled events (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5qh6 | ||||||
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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 NUOOA000259a | ||||||
Components | Peroxisomal coenzyme A diphosphatase NUDT7 | ||||||
Keywords | HYDROLASE / PanDDA / SGC - Diamond I04-1 fragment screening / NUDIX domain / XChemExplorer | ||||||
Function / homology | Function and homology information butyryl-CoA catabolic process / propionyl-CoA metabolic process / propionyl-CoA catabolic process / medium-chain fatty-acyl-CoA catabolic process / malonyl-CoA catabolic process / Peroxisomal lipid metabolism / coenzyme A diphosphatase activity / coenzyme A catabolic process / acetyl-CoA catabolic process / succinyl-CoA catabolic process ...butyryl-CoA catabolic process / propionyl-CoA metabolic process / propionyl-CoA catabolic process / medium-chain fatty-acyl-CoA catabolic process / malonyl-CoA catabolic process / Peroxisomal lipid metabolism / coenzyme A diphosphatase activity / coenzyme A catabolic process / acetyl-CoA catabolic process / succinyl-CoA catabolic process / nucleoside diphosphate metabolic process / snoRNA binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / peroxisomal matrix / brown fat cell differentiation / Peroxisomal protein import / peroxisome / manganese ion binding / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2 Å | ||||||
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. ...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. | ||||||
Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5qh6.cif.gz | 57.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5qh6.ent.gz | 40.1 KB | Display | PDB format |
PDBx/mmJSON format | 5qh6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5qh6_validation.pdf.gz | 458.2 KB | Display | wwPDB validaton report |
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Full document | 5qh6_full_validation.pdf.gz | 458.4 KB | Display | |
Data in XML | 5qh6_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 5qh6_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/5qh6 ftp://data.pdbj.org/pub/pdb/validation_reports/qh/5qh6 | HTTPS FTP |
-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: 10.5281/zenodo.1244111 / Data set type: other data / Details: Complete PanDDA analysis / Metadata reference: 10.5281/zenodo.1244111 |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: NUDT7 / Production host: Escherichia coli (E. coli) References: UniProt: P0C024, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-H0M / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.11 Å3/Da / Density % sol: 70.08 % / Mosaicity: 0 ° |
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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: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.57→62.1 Å / Num. obs: 50805 / % possible obs: 100 % / Redundancy: 9.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.019 / Rrim(I) all: 0.059 / Net I/σ(I): 18.5 / Num. measured all: 500488 / 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: 5T3P Resolution: 2→107.56 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.46 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.117 / 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: 105.15 Å2 / Biso mean: 32.872 Å2 / Biso min: 17.26 Å2
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Refinement step | Cycle: final / Resolution: 2→107.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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