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Yorodumi- PDB-6iu9: Crystal structure of cytoplasmic metal binding domain with iron ions -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iu9 | ||||||
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Title | Crystal structure of cytoplasmic metal binding domain with iron ions | ||||||
Components | VIT1 | ||||||
Keywords | METAL TRANSPORT / membrane protein | ||||||
Function / homology | : Function and homology information | ||||||
Biological species | Eucalyptus grandis (rose gum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Kato, T. / Nishizawa, T. / Yamashita, K. / Kumazaki, K. / Ishitani, R. / Nureki, O. | ||||||
Citation | Journal: Nat Plants / Year: 2019 Title: Crystal structure of plant vacuolar iron transporter VIT1. Authors: Kato, T. / Kumazaki, K. / Wada, M. / Taniguchi, R. / Nakane, T. / Yamashita, K. / Hirata, K. / Ishitani, R. / Ito, K. / Nishizawa, T. / Nureki, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iu9.cif.gz | 135.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iu9.ent.gz | 104.9 KB | Display | PDB format |
PDBx/mmJSON format | 6iu9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/6iu9 ftp://data.pdbj.org/pub/pdb/validation_reports/iu/6iu9 | HTTPS FTP |
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-Related structure data
Related structure data | 6iu3C 6iu4C 6iu5SC 6iu6C 6iu8C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.2532134 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 9106.312 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eucalyptus grandis (rose gum) / Plasmid: modified pE-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-FE2 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.3 % / Mosaicity: 0.11 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 21-23% PEG600, 0.1 M HEPES pH7.0 and 0.001-0.003 M zinc cloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.74 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 5, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.74 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 3→42.6607 Å / Num. obs: 15910 / % possible obs: 99.9937 % / Redundancy: 5.139 % / CC1/2: 0.9848 / Rmerge(I) obs: 0.2096 / Rpim(I) all: 0.1035 / Rrim(I) all: 0.2342 / Net I/σ(I): 5.9655 / Num. measured all: 81761 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IU5 Resolution: 3→42.66 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.911 / SU B: 14.075 / SU ML: 0.277 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.096 / 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: 234.97 Å2 / Biso mean: 94.125 Å2 / Biso min: 24.9 Å2
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Refinement step | Cycle: final / Resolution: 3→42.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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