+Open data
-Basic information
Entry | Database: PDB / ID: 3h7g | ||||||
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Title | Apo-FR with AU ions | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL BINDING PROTEIN / IRON STORAGE / LIGHT CHAIN APOFERRITIN / Iron | ||||||
Function / homology | Function and homology information : / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Abe, M. / Ueno, T. / Abe, S. / Suzuki, M. / Goto, T. / Toda, Y. / Akita, T. / Yamada, Y. / Watanabe, Y. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2009 Title: Preparation and catalytic reaction of Au/Pd bimetallic nanoparticles in apo-ferritin Authors: Suzuki, M. / Abe, M. / Ueno, T. / Abe, S. / Goto, T. / Toda, Y. / Akita, T. / Yamada, Y. / Watanabe, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h7g.cif.gz | 56.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h7g.ent.gz | 41.2 KB | Display | PDB format |
PDBx/mmJSON format | 3h7g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3h7g_validation.pdf.gz | 445.9 KB | Display | wwPDB validaton report |
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Full document | 3h7g_full_validation.pdf.gz | 446.4 KB | Display | |
Data in XML | 3h7g_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 3h7g_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/3h7g ftp://data.pdbj.org/pub/pdb/validation_reports/h7/3h7g | HTTPS FTP |
-Related structure data
Related structure data | 1datS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 19856.385 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Plasmid: PMK2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NOVA BLUE / References: UniProt: P02791 |
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-Non-polymers , 5 types, 193 molecules
#2: Chemical | ChemComp-AU3 / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | REFER TO THE DATABASE, P02791, REF. 2 FOR THIS CONFLICT. THIS SEQUENCE IS FROM BAA03396 IN GENBANK DATABASE. |
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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: 3.14 Å3/Da / Density % sol: 60.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: AMMONIUM SULFATE, CADMIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.65→35 Å / Num. obs: 31508 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 20.2 % / Biso Wilson estimate: 16.79 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 67.8 | ||||||||||||||||||
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 14 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 8.01 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DAT Resolution: 1.65→30.28 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.912 / SU B: 1.25 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→30.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.69 Å / Total num. of bins used: 20
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