+Open data
-Basic information
Entry | Database: PDB / ID: 4x82 | ||||||
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Title | Crystal Structure of the Extracellular Domain of ZIP4 | ||||||
Components | Zinc transporter ZIP4 | ||||||
Keywords | TRANSPORT PROTEIN / zinc transporter / extracellular domain | ||||||
Function / homology | Zinc transporter ZIP4, N-terminal / Zinc transporter ZIP4 domain / Zinc/iron permease / ZIP Zinc transporter / metal ion transmembrane transporter activity / membrane => GO:0016020 / Zinc transporter ZIP4 Function and homology information | ||||||
Biological species | Pteropus alecto (black flying fox) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.76 Å | ||||||
Authors | Zhang, T. / Sui, D.X. / Hu, J. | ||||||
Citation | Journal: Nat Commun / Year: 2016 Title: Structural insights of ZIP4 extracellular domain critical for optimal zinc transport. Authors: Zhang, T. / Sui, D. / Hu, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x82.cif.gz | 87 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x82.ent.gz | 69.1 KB | Display | PDB format |
PDBx/mmJSON format | 4x82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/4x82 ftp://data.pdbj.org/pub/pdb/validation_reports/x8/4x82 | HTTPS FTP |
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-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:
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-Components
#1: Protein | Mass: 30065.699 Da / Num. of mol.: 2 / Fragment: Residues 36-322 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pteropus alecto (black flying fox) / Gene: PAL_GLEAN10010497 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami (DE3) / References: UniProt: L5KLU7 |
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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: 1.83 Å3/Da / Density % sol: 32.65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 18% PEG 3350, 50 mM NH4Cl |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 25, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.76→40 Å / Num. obs: 11028 / % possible obs: 99.4 % / Redundancy: 21.7 % / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.038 / Rrim(I) all: 0.179 / Χ2: 0.986 / Net I/av σ(I): 20.885 / Net I/σ(I): 5.4 / Num. measured all: 239259 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Resolution: 2.76→38.65 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.908 / SU B: 17.742 / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.423 / 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: 139.63 Å2 / Biso mean: 58.555 Å2 / Biso min: 33.03 Å2
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Refinement step | Cycle: final / Resolution: 2.76→38.65 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 9067 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.764→2.835 Å / Total num. of bins used: 20
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