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Yorodumi- PDB-5yxc: Crystal structure of Zinc binding protein ZinT in complex with ci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yxc | |||||||||||||||
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Title | Crystal structure of Zinc binding protein ZinT in complex with citrate from E. coli | |||||||||||||||
Components | Metal-binding protein ZinT | |||||||||||||||
Keywords | METAL BINDING PROTEIN / Zinc binding protein / complex / citrate | |||||||||||||||
Function / homology | Function and homology information cellular response to zinc ion starvation / intracellular zinc ion homeostasis / cadmium ion binding / cellular response to cadmium ion / cellular response to hydrogen peroxide / outer membrane-bounded periplasmic space / zinc ion binding / metal ion binding / cytosol Similarity search - Function | |||||||||||||||
Biological species | Escherichia coli (E. coli) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.763 Å | |||||||||||||||
Authors | Chen, J. / Wang, L. / Shang, F. / Xu, Y. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2018 Title: Crystal structure of E. coli ZinT with one zinc-binding mode and complexed with citrate Authors: Chen, J. / Wang, L. / Shang, F. / Dong, Y. / Ha, N.C. / Nam, K.H. / Quan, C. / Xu, Y. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yxc.cif.gz | 163.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yxc.ent.gz | 129.8 KB | Display | PDB format |
PDBx/mmJSON format | 5yxc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/5yxc ftp://data.pdbj.org/pub/pdb/validation_reports/yx/5yxc | HTTPS FTP |
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-Related structure data
Related structure data | 4aw8S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24795.865 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: zinT, yodA, b1973, JW1956 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P76344 #2: Chemical | #3: Chemical | #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: 2.01 Å3/Da / Density % sol: 38.67 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 22.5%(w/v) polyethylene glycol 4000, 0.135M ammonium acetate, and 0.1M sodium acetate trihydrate (pH 4.6) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9826 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9826 Å / Relative weight: 1 |
Reflection | Resolution: 1.763→41.029 Å / Num. obs: 37131 / % possible obs: 90.5 % / Redundancy: 2.2 % / Rsym value: 0.097 / Net I/σ(I): 0.1 |
Reflection shell | Resolution: 1.763→1.79 Å / Num. unique obs: 1828 / Rsym value: 0.22 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4AW8 Resolution: 1.763→41.029 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.56 / Phase error: 24.9
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.763→41.029 Å
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Refine LS restraints |
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LS refinement shell |
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