[English] 日本語
Yorodumi- PDB-5qib: PanDDA analysis group deposition of models with modelled events (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5qib | ||||||
---|---|---|---|---|---|---|---|
Title | PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of HAO1 in complex with FMOPL000388a | ||||||
Components | Hydroxyacid oxidase 1 | ||||||
Keywords | OXIDOREDUCTASE / PanDDA / SGC - Diamond I04-1 fragment screening / HAO1 / XChemExplorer | ||||||
Function / homology | Function and homology information glyoxylate oxidase / glyoxylate oxidase activity / glycolate catabolic process / (S)-2-hydroxy-acid oxidase / (S)-2-hydroxy-acid oxidase activity / fatty acid alpha-oxidation / Glyoxylate metabolism and glycine degradation / glycine biosynthetic process / peroxisomal matrix / Peroxisomal protein import ...glyoxylate oxidase / glyoxylate oxidase activity / glycolate catabolic process / (S)-2-hydroxy-acid oxidase / (S)-2-hydroxy-acid oxidase activity / fatty acid alpha-oxidation / Glyoxylate metabolism and glycine degradation / glycine biosynthetic process / peroxisomal matrix / Peroxisomal protein import / FMN binding / response to oxidative stress / intracellular membrane-bounded organelle / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.48 Å | ||||||
Authors | MacKinnon, S. / Bezerra, G.A. / Krojer, T. / Bradley, A.R. / Talon, R. / Brandao-Neto, J. / Douangamath, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. ...MacKinnon, S. / Bezerra, G.A. / Krojer, T. / Bradley, A.R. / Talon, R. / Brandao-Neto, J. / Douangamath, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Oppermann, U. / Brennan, P.E. / Yue, W.W. | ||||||
Citation | Journal: To Be Published Title: PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) Authors: MacKinnon, S. / Bezerra, G.A. / Krojer, T. / Bradley, A.R. / Talon, R. / Brandao-Neto, J. / Douangamath, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Oppermann, U. / ...Authors: MacKinnon, S. / Bezerra, G.A. / Krojer, T. / Bradley, A.R. / Talon, R. / Brandao-Neto, J. / Douangamath, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Oppermann, U. / Brennan, P.E. / Yue, W.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5qib.cif.gz | 99.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5qib.ent.gz | 77.3 KB | Display | PDB format |
PDBx/mmJSON format | 5qib.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/5qib ftp://data.pdbj.org/pub/pdb/validation_reports/qi/5qib | HTTPS FTP |
---|
-Group deposition
ID | G_1002048 (7 entries) |
---|---|
Title | PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) |
Type | changed state |
Description | human HAO1 screened against the DSPL Fragment Library by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1 |
-Related structure data
Related structure data | 2nzlS S: Starting model for refinement |
---|---|
Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.1249653 / Data set type: other data / Details: Complete PanDDA analysis / Metadata reference: 10.5281/zenodo.1249653 |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 40820.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HAO1, GOX1, HAOX1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UJM8, (S)-2-hydroxy-acid oxidase |
---|---|
#2: Chemical | ChemComp-FNR / |
#3: Chemical | ChemComp-GX7 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.83 % / Mosaicity: 0.07 ° |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.75 / Details: 0.1M MIB pH 5.75 - 7.0, 27.5-35% PEG1000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.48→26.43 Å / Num. obs: 64140 / % possible obs: 99.4 % / Redundancy: 6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.016 / Rrim(I) all: 0.042 / Net I/σ(I): 24.5 / Num. measured all: 385802 / Scaling rejects: 0 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2NZL Resolution: 1.48→69.29 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.611 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 58.4 Å2 / Biso mean: 19.462 Å2 / Biso min: 8.72 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.48→69.29 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.478→1.517 Å / Total num. of bins used: 20
|