+Open data
-Basic information
Entry | Database: PDB / ID: 5zle | ||||||||||||
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Title | Human duodenal cytochrome b (Dcytb) in substrate free form | ||||||||||||
Components | Cytochrome b reductase 1 | ||||||||||||
Keywords | OXIDOREDUCTASE / electron transport | ||||||||||||
Function / homology | Function and homology information transmembrane monodehydroascorbate reductase activity / ascorbate homeostasis / ascorbate ferrireductase (transmembrane) / transmembrane ascorbate ferrireductase activity / reductive iron assimilation / : / oxidoreductase activity, acting on metal ions / response to iron ion / brush border membrane / Iron uptake and transport ...transmembrane monodehydroascorbate reductase activity / ascorbate homeostasis / ascorbate ferrireductase (transmembrane) / transmembrane ascorbate ferrireductase activity / reductive iron assimilation / : / oxidoreductase activity, acting on metal ions / response to iron ion / brush border membrane / Iron uptake and transport / intracellular iron ion homeostasis / oxidoreductase activity / apical plasma membrane / lysosomal membrane / extracellular exosome / membrane / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||||||||
Model details | Ascorbate-dependent ferric reductase Dcytb | ||||||||||||
Authors | Ganasen, M. / Togashi, H. / Mauk, G.A. / Shiro, Y. / Sawai, H. / Sugimoto, H. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Commun Biol / Year: 2018 Title: Structural basis for promotion of duodenal iron absorption by enteric ferric reductase with ascorbate. Authors: Ganasen, M. / Togashi, H. / Takeda, H. / Asakura, H. / Tosha, T. / Yamashita, K. / Hirata, K. / Nariai, Y. / Urano, T. / Yuan, X. / Hamza, I. / Mauk, A.G. / Shiro, Y. / Sugimoto, H. / Sawai, H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zle.cif.gz | 110.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zle.ent.gz | 83.2 KB | Display | PDB format |
PDBx/mmJSON format | 5zle.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/5zle ftp://data.pdbj.org/pub/pdb/validation_reports/zl/5zle | HTTPS FTP |
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-Related structure data
Related structure data | 5zlgC 4o7gS 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: 32362.033 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYBRD1, DCYTB, FRRS3 / Plasmid: pET-21b / Production host: Escherichia coli BL21 Star (DE3) (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: Q53TN4, Oxidoreductases | ||
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#2: Chemical | #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: 2.45 Å3/Da / Density % sol: 49.75 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 6.5 / Details: 20%(v/v) Jeffamine ED-2003, 0.1 M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 22, 2016 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→42.935 Å / Num. obs: 9644 / % possible obs: 99.3 % / Redundancy: 72.377 % / Biso Wilson estimate: 26.85 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.0103 / Rrim(I) all: 0.01037 / Χ2: 1.432 / Net I/σ(I): 9.96 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4O7G Resolution: 2.6→42.935 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.3
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.38 Å2 / Biso mean: 33.6033 Å2 / Biso min: 5.28 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→42.935 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 13.371 Å / Origin y: 36.243 Å / Origin z: 11.459 Å
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Refinement TLS group |
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