+Open data
-Basic information
Entry | Database: PDB / ID: 3noz | ||||||
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Title | Crystal Structure of Pd(allyl)/apo-E45C/R52H-rHLFr | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL BINDING PROTEIN | ||||||
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: 1.52 Å | ||||||
Authors | Wang, Z. / Ueno, T. / Abe, S. / Takezawa, Y. / Aoyagi, H. / Hikage, T. / Watanabe, Y. / Kitagawa, S. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2011 Title: Definite coordination arrangement of organometallic palladium complexes accumulated on the designed interior surface of apo-ferritin. Authors: Wang, Z. / Takezawa, Y. / Aoyagi, H. / Abe, S. / Hikage, T. / Watanabe, Y. / Kitagawa, S. / Ueno, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3noz.cif.gz | 58.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3noz.ent.gz | 42.8 KB | Display | PDB format |
PDBx/mmJSON format | 3noz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/3noz ftp://data.pdbj.org/pub/pdb/validation_reports/no/3noz | HTTPS FTP |
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-Related structure data
Related structure data | 3np0C 3np2C 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: 19827.410 Da / Num. of mol.: 1 / Mutation: E45C, R52H 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 , 5 types, 190 molecules
#2: Chemical | ChemComp-SO4 / | ||||
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#3: Chemical | ChemComp-CD / | ||||
#4: Chemical | ChemComp-PLL / #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
-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: 60.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: ammonium sulfate, cadmium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2009 |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→25 Å / Num. obs: 39501 / % possible obs: 99.2 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.054 |
Reflection shell | Resolution: 1.52→1.57 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.347 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DAT Resolution: 1.52→19.34 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.116 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 18.485 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.52→19.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.52→1.559 Å / Total num. of bins used: 20
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