+Open data
-Basic information
Entry | Database: PDB / ID: 2zg8 | ||||||
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Title | Crystal Structure of Pd(allyl)/apo-H49AFr | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL BINDING PROTEIN / IRON STORAGE PROTEIN / LIGHT CHAIN APOFERRITIN / ARTIFICIAL METALLOPROTEIN | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Abe, S. / Niemeyer, J. / Abe, M. / Ueno, T. / Hikage, T. / Erker, G. / Watanabe, Y. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2008 Title: Control of the coordination structure of organometallic palladium complexes in an apo-ferritin cage. Authors: Abe, S. / Niemeyer, J. / Abe, M. / Takezawa, Y. / Ueno, T. / Hikage, T. / Erker, G. / Watanabe, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zg8.cif.gz | 58.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zg8.ent.gz | 43 KB | Display | PDB format |
PDBx/mmJSON format | 2zg8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zg8_validation.pdf.gz | 464.7 KB | Display | wwPDB validaton report |
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Full document | 2zg8_full_validation.pdf.gz | 466.1 KB | Display | |
Data in XML | 2zg8_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 2zg8_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/2zg8 ftp://data.pdbj.org/pub/pdb/validation_reports/zg/2zg8 | HTTPS FTP |
-Related structure data
Related structure data | 2zg7C 2zg9C 1datS C: citing same article (ref.) 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules X
#1: Protein | Mass: 19789.314 Da / Num. of mol.: 1 / Mutation: H49A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Gene: FTL / Plasmid: pMK2 / Production host: Escherichia coli (E. coli) / Strain (production host): Nova Blue / References: UniProt: P02791 |
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-Non-polymers , 6 types, 227 molecules
#2: Chemical | ChemComp-PD / | ||||||
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#3: Chemical | ChemComp-CD / | ||||||
#4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | IN THE LIGAND PLL, ALL C-C BOND TYPES ARE DELOCALIZESequence details | THE FEATURE OF UNIPROT (FRIL_HORSE, P02791) SHOWS CONFLICT AT THIS POSITION: L -> P (IN REF. 2). | |
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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: 60.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: ammonium sulfate, cadmium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Aug 20, 2007 |
Radiation | Monochromator: CONFOCAL MIRROS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 34183 / % possible obs: 100 % / Redundancy: 17.8 % / Biso Wilson estimate: 18.007 Å2 / Rmerge(I) obs: 0.062 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.284 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DAT Resolution: 1.6→25.15 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.168 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.079 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.223 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→25.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.601→1.642 Å / Total num. of bins used: 20
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