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Yorodumi- PDB-1zpu: Crystal Structure of Fet3p, a Multicopper Oxidase that Functions ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zpu | |||||||||
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Title | Crystal Structure of Fet3p, a Multicopper Oxidase that Functions in Iron Import | |||||||||
Components | Iron transport multicopper oxidase FET3 | |||||||||
Keywords | OXIDOREDUCTASE / multicopper oxidase / ferroxidase / iron transport | |||||||||
Function / homology | Function and homology information high-affinity iron permease complex / iron ion import across cell outer membrane / arsenate ion transmembrane transport / reductive iron assimilation / oxidoreductase activity, acting on metal ions, oxygen as acceptor / cuproxidase / cellular response to iron ion starvation / iron ion transmembrane transport / fungal-type vacuole / response to copper ion ...high-affinity iron permease complex / iron ion import across cell outer membrane / arsenate ion transmembrane transport / reductive iron assimilation / oxidoreductase activity, acting on metal ions, oxygen as acceptor / cuproxidase / cellular response to iron ion starvation / iron ion transmembrane transport / fungal-type vacuole / response to copper ion / ferroxidase / intracellular copper ion homeostasis / ferroxidase activity / intracellular iron ion homeostasis / copper ion binding / endoplasmic reticulum / plasma membrane Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | |||||||||
Authors | Taylor, A.B. / Stoj, C.S. / Ziegler, L. / Kosman, D.J. / Hart, P.J. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2005 Title: The copper-iron connection in biology: Structure of the metallo-oxidase Fet3p. Authors: Taylor, A.B. / Stoj, C.S. / Ziegler, L. / Kosman, D.J. / Hart, P.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zpu.cif.gz | 644.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zpu.ent.gz | 548.1 KB | Display | PDB format |
PDBx/mmJSON format | 1zpu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zpu_validation.pdf.gz | 12 MB | Display | wwPDB validaton report |
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Full document | 1zpu_full_validation.pdf.gz | 12.1 MB | Display | |
Data in XML | 1zpu_validation.xml.gz | 72.9 KB | Display | |
Data in CIF | 1zpu_validation.cif.gz | 106.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/1zpu ftp://data.pdbj.org/pub/pdb/validation_reports/zp/1zpu | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: GLU / End label comp-ID: ALA / Refine code: 2 / Auth seq-ID: 22 - 550 / Label seq-ID: 1 - 529
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-Components
-Protein / Non-polymers , 2 types, 30 molecules ABCDEF
#1: Protein | Mass: 60859.156 Da / Num. of mol.: 6 / Fragment: Fet3p ectodomain (residues 22-555) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: FET3 / Plasmid: pDY148 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): M2* / References: UniProt: P38993, Oxidoreductases #9: Chemical | ChemComp-CU1 / |
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-Sugars , 7 types, 63 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #5: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-NAG / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: sodium citrate, HEPES, ethylene glycol, ethanol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.8→50 Å / Num. all: 136782 / Num. obs: 136782 / % possible obs: 99.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 68.6 Å2 / Rsym value: 0.081 / Net I/σ(I): 14.9 | |||||||||||||||
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 20049 / Rsym value: 0.36 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.908 / SU B: 35.47 / SU ML: 0.299 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic (NCS-restrained) / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.829 / ESU R Free: 0.344 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.824 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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