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Yorodumi- PDB-6kh3: Design and crystal structure of protein MOFs with ferritin nanoca... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kh3 | |||||||||
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Title | Design and crystal structure of protein MOFs with ferritin nanocages as linkers and nickel clusters as nodes | |||||||||
Components | Ferritin | |||||||||
Keywords | METAL BINDING PROTEIN / protein MOF / ferritin / Nickel | |||||||||
Function / homology | Function and homology information ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / cytosol Similarity search - Function | |||||||||
Biological species | Penaeus japonicus (crustacean) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Gu, C. / Chen, H. / Wang, Y. / Zhang, T. / Wang, H. / Zhao, G. | |||||||||
Funding support | China, 2items
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Citation | Journal: Chemistry / Year: 2020 Title: Structural Insight into Binary Protein Metal-Organic Frameworks with Ferritin Nanocages as Linkers and Nickel Clusters as Nodes. Authors: Gu, C. / Chen, H. / Wang, Y. / Zhang, T. / Wang, H. / Zhao, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kh3.cif.gz | 82.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kh3.ent.gz | 61.8 KB | Display | PDB format |
PDBx/mmJSON format | 6kh3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kh3_validation.pdf.gz | 685.3 KB | Display | wwPDB validaton report |
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Full document | 6kh3_full_validation.pdf.gz | 686.2 KB | Display | |
Data in XML | 6kh3_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 6kh3_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/6kh3 ftp://data.pdbj.org/pub/pdb/validation_reports/kh/6kh3 | HTTPS FTP |
-Related structure data
Related structure data | 6kh0C 6kh1C 6kh4C 6kh5C 6a4uS 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: 19534.824 Da / Num. of mol.: 1 / Mutation: T161H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Penaeus japonicus (crustacean) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: T2B7E1, ferroxidase |
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#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-NI / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.59 Å3/Da / Density % sol: 65.73 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 1 M NH4H2PO4, 100 mM Tris ( pH = 8.5 ) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.4938 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 3, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.4938 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 24213 / % possible obs: 99.9 % / Redundancy: 22.3 % / Rmerge(I) obs: 0.226 / Rpim(I) all: 0.049 / Rrim(I) all: 0.232 / Χ2: 0.898 / Net I/σ(I): 6.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6A4U Resolution: 2.3→39.647 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 19.46
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.48 Å2 / Biso mean: 36.5897 Å2 / Biso min: 18.27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→39.647 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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