+Open data
-Basic information
Entry | Database: PDB / ID: 6l58 | ||||||
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Title | Cu(II) loaded Tegillarca granosa M-ferritin soaked with Fe(II) | ||||||
Components | Ferritin | ||||||
Keywords | OXIDOREDUCTASE / ferritin / copper / tegillarca granosa / Structural Genomics / Center for Eukaryotic Structural Genomics / CESG | ||||||
Function / homology | Function and homology information ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis Similarity search - Function | ||||||
Biological species | Tegillarca granosa (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.90270963518 Å | ||||||
Authors | Jiang, Q.Q. / Su, X.R. / Ming, T.H. / Huan, H.S. | ||||||
Citation | Journal: Front Mol Biosci / Year: 2022 Title: Structural Insights Into the Effects of Interactions With Iron and Copper Ions on Ferritin From the Blood Clam Tegillarca granosa. Authors: Ming, T.H. / Jiang, Q.Q. / Huo, C. / Huan, H.S. / Wu, Y. / Su, C. / Qiu, X. / Lu, C. / Zhou, J. / Li, Y. / Han, J. / Zhang, Z. / Su, X.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l58.cif.gz | 169.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l58.ent.gz | 107.3 KB | Display | PDB format |
PDBx/mmJSON format | 6l58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l5/6l58 ftp://data.pdbj.org/pub/pdb/validation_reports/l5/6l58 | HTTPS FTP |
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-Related structure data
Related structure data | 6kzyC 6l55C 6l56C 3a9kS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 20020.438 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tegillarca granosa (invertebrata) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D3JCC5, ferroxidase #2: Chemical | ChemComp-CU / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.8 Å3/Da / Density % sol: 67.66 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M ammonium acetate, 0.1M TRIS hydrochloride pH 7.5, a precipitant solution of 30% v/v 2-Propanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.7389 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7389 Å / Relative weight: 1 |
Reflection | Resolution: 3.9→50 Å / Num. obs: 10532 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 72.3114190968 Å2 / Rmerge(I) obs: 0.167 / Rsym value: 0.167 / Net I/σ(I): 10.357 |
Reflection shell | Resolution: 3.9→3.97 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 412 / CC1/2: 0.523 / % possible all: 73.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3A9K Resolution: 3.90270963518→36.3993584617 Å / SU ML: 0.482757452022 / Cross valid method: FREE R-VALUE / σ(F): 1.34370859458 / Phase error: 30.8101531862
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.1958603175 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.90270963518→36.3993584617 Å
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Refine LS restraints |
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LS refinement shell |
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