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Yorodumi- PDB-6gmc: 1.2 A resolution structure of human hydroxyacid oxidase 1 bound w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gmc | |||||||||
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Title | 1.2 A resolution structure of human hydroxyacid oxidase 1 bound with FMN and 4-carboxy-5-[(4-chlorophenyl)sulfanyl]-1,2,3-thiadiazole | |||||||||
Components | Hydroxyacid oxidase 1 | |||||||||
Keywords | OXIDOREDUCTASE / glycolate / glyoxylate / peroxisome / FMN / primary hyperoxaluria | |||||||||
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: 1.2 Å | |||||||||
Authors | MacKinnon, S. / Bezerra, G.A. / Krojer, T. / Smee, C. / Arrowsmith, C.H. / Edwards, E. / 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 FMN and glycolate Authors: MacKinnon, S. / Bezerra, G.A. / Krojer, T. / Smee, C. / Arrowsmith, C.H. / Edwards, E. / 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 | 6gmc.cif.gz | 175.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gmc.ent.gz | 137.1 KB | Display | PDB format |
PDBx/mmJSON format | 6gmc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gmc_validation.pdf.gz | 1021.5 KB | Display | wwPDB validaton report |
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Full document | 6gmc_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6gmc_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 6gmc_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/6gmc ftp://data.pdbj.org/pub/pdb/validation_reports/gm/6gmc | HTTPS FTP |
-Related structure data
Related structure data | 6gmbC 2nzlS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40733.918 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 | ||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-FMN / | #4: Chemical | ChemComp-C7C / | #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: 2.38 Å3/Da / Density % sol: 48.36 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 20% PEG3350 -- 10% ethylene glycol -- 0.1M bis-tris-propane pH 7.5 -- 0.2M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 2, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→68.835 Å / Num. all: 115996 / Num. obs: 115996 / % possible obs: 99.5 % / Redundancy: 4.2 % / Rpim(I) all: 0.042 / Rrim(I) all: 0.088 / Rsym value: 0.076 / Net I/av σ(I): 4.3 / Net I/σ(I): 8.9 / Num. measured all: 484713 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2NZL Resolution: 1.2→38.31 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.144 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.033 / 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: 62.97 Å2 / Biso mean: 16.823 Å2 / Biso min: 6.83 Å2
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Refinement step | Cycle: final / Resolution: 1.2→38.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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