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Yorodumi- PDB-7r4p: Structure of human hydroxyacid oxidase 1 bound with 6-amino-1-ben... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7r4p | ||||||
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Title | Structure of human hydroxyacid oxidase 1 bound with 6-amino-1-benzyl-5-(methylamino)pyrimidine-2,4(1H,3H)-dione | ||||||
Components | Hydroxyacid oxidase 1 | ||||||
Keywords | OXIDOREDUCTASE / HAO1 / hydroxyacid oxidase / glycolate oxidase / fragment screening | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.37 Å | ||||||
Authors | Mackinnon, S. / Bezerra, G.A. / Krojer, T. / Bradley, A.R. / Talon, R. / Brandeo-Neto, J. / Douangamath, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. ...Mackinnon, S. / Bezerra, G.A. / Krojer, T. / Bradley, A.R. / Talon, R. / Brandeo-Neto, J. / Douangamath, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Oppermann, U. / Brennan, P.E. / Yue, W.W. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Structure of human hydroxyacid oxidase 1 bound with 5-bromo-N-methyl-1H-indazole-3-carboxamide Authors: Mackinnon, S. / Bezerra, G.A. / Krojer, T. / Bradley, A.R. / Talon, R. / Brandeo-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. / Brandeo-Neto, J. / Douangamath, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Oppermann, U. / Brennan, P.E. / Yue, W.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7r4p.cif.gz | 151.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7r4p.ent.gz | 116.7 KB | Display | PDB format |
PDBx/mmJSON format | 7r4p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7r4p_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7r4p_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7r4p_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 7r4p_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/7r4p ftp://data.pdbj.org/pub/pdb/validation_reports/r4/7r4p | HTTPS FTP |
-Related structure data
Related structure data | 7r4nC 7r4oC 6gmbS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40152.258 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 BL21(DE3) (bacteria) / References: UniProt: Q9UJM8, (S)-2-hydroxy-acid oxidase |
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#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-I2Z / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M MIB, pH 7, 30% PEG1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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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: Jul 2, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.37→68.68 Å / Num. obs: 77168 / % possible obs: 98.1 % / Redundancy: 5.5 % / CC1/2: 1 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.014 / Rrim(I) all: 0.036 / Net I/σ(I): 20.3 / Num. measured all: 424652 / Scaling rejects: 9 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GMB Resolution: 1.37→68.68 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.082 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 65.29 Å2 / Biso mean: 22.088 Å2 / Biso min: 12.41 Å2
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Refinement step | Cycle: final / Resolution: 1.37→68.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.37→1.406 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 14.6302 Å / Origin y: 25.6739 Å / Origin z: 23.4868 Å
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