+Open data
-Basic information
Entry | Database: PDB / ID: 3u2l | ||||||
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Title | Crystal structure of human ALR mutant C142S. | ||||||
Components | FAD-linked sulfhydryl oxidase ALR | ||||||
Keywords | FLAVOPROTEIN / ALR / Sulfhydryl oxidase / Flavin / FAD | ||||||
Function / homology | Function and homology information flavin-dependent sulfhydryl oxidase activity / thiol oxidase / cellular response to toxic substance / negative regulation of natural killer cell mediated cytotoxicity / Mitochondrial protein import / positive regulation of DNA biosynthetic process / protein-disulfide reductase activity / cellular response to actinomycin D / liver development / liver regeneration ...flavin-dependent sulfhydryl oxidase activity / thiol oxidase / cellular response to toxic substance / negative regulation of natural killer cell mediated cytotoxicity / Mitochondrial protein import / positive regulation of DNA biosynthetic process / protein-disulfide reductase activity / cellular response to actinomycin D / liver development / liver regeneration / growth factor activity / mitochondrial intermembrane space / cellular response to tumor necrosis factor / flavin adenine dinucleotide binding / cellular response to lipopolysaccharide / negative regulation of apoptotic process / mitochondrion / extracellular space / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Banci, L. / Bertini, I. / Calderone, V. / Cefaro, C. / Ciofi-Baffoni, S. / Gallo, A. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2012 Title: An electron-transfer path through an extended disulfide relay system: the case of the redox protein ALR. Authors: Banci, L. / Bertini, I. / Calderone, V. / Cefaro, C. / Ciofi-Baffoni, S. / Gallo, A. / Tokatlidis, K. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Molecular recognition and substrate mimicry drive the electron-transfer process between MIA40 and ALR. Authors: Banci, L. / Bertini, I. / Calderone, V. / Cefaro, C. / Ciofi-Baffoni, S. / Gallo, A. / Kallergi, E. / Lionaki, E. / Pozidis, C. / Tokatlidis, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u2l.cif.gz | 42.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u2l.ent.gz | 28.7 KB | Display | PDB format |
PDBx/mmJSON format | 3u2l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3u2l_validation.pdf.gz | 820.3 KB | Display | wwPDB validaton report |
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Full document | 3u2l_full_validation.pdf.gz | 822.6 KB | Display | |
Data in XML | 3u2l_validation.xml.gz | 9 KB | Display | |
Data in CIF | 3u2l_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u2/3u2l ftp://data.pdbj.org/pub/pdb/validation_reports/u2/3u2l | HTTPS FTP |
-Related structure data
Related structure data | 3u2mC 3o55S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 13698.232 Da / Num. of mol.: 1 / Fragment: unp residues 91-205 / Mutation: C142S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GFER, ALR, HERV1, HPO / Plasmid: pDEST-His-MBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P55789, thiol oxidase |
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#2: Chemical | ChemComp-FAD / |
#3: 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: 2.23 Å3/Da / Density % sol: 44.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1 M MES, 20% PEG6000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.541 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Jul 14, 2010 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25.45 Å / Num. all: 9237 / Num. obs: 9237 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.3 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1312 / Rsym value: 0.44 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3O55 Resolution: 1.95→25.45 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.888 / SU B: 4.321 / SU ML: 0.126 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.759 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→25.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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