+Open data
-Basic information
Entry | Database: PDB / ID: 3np0 | ||||||
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Title | Crystal Structure of Pd(allyl)/apo-E45C/H49A/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: 1.48 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 | 3np0.cif.gz | 58.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3np0.ent.gz | 42.9 KB | Display | PDB format |
PDBx/mmJSON format | 3np0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/3np0 ftp://data.pdbj.org/pub/pdb/validation_reports/np/3np0 | HTTPS FTP |
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-Related structure data
Related structure data | 3nozC 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: 19760.340 Da / Num. of mol.: 1 / Mutation: E45C, H49A, 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, 228 molecules
#2: Chemical | #3: Chemical | ChemComp-PLL / #4: Chemical | ChemComp-CD / | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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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: 3.12 Å3/Da / Density % sol: 60.62 % |
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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: 1.48→30 Å / Num. obs: 41911 / % possible obs: 98.3 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.064 |
Reflection shell | Resolution: 1.48→1.53 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.286 / % possible all: 88.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DAT Resolution: 1.48→19.29 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.947 / SU B: 0.945 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R Free: 0.066 / 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: 16.578 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.48→19.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.481→1.52 Å / Total num. of bins used: 20
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