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Yorodumi- PDB-2za7: recombinant horse L-chain apoferritin N-terminal deletion mutant ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2za7 | ||||||
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Title | recombinant horse L-chain apoferritin N-terminal deletion mutant (residues 1-4) | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL BINDING PROTEIN / ferric iron binding / Acetylation / Iron storage / Metal-binding | ||||||
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: 1.4 Å | ||||||
Authors | Yamashita, I. / Mishima, Y. / Park, S.-Y. / Heddle, J.G. / Tame, J.R.H. | ||||||
Citation | Journal: J.BIOCHEM.(TOKYO) / Year: 2007 Title: Effect of N-terminal Residues on the Structural Stability of Recombinant Horse L-chain Apoferritin in an Acidic Environment Authors: Yoshizawa, K. / Mishima, Y. / Park, S.-Y. / Heddle, J.G. / Tame, J.R.H. / Iwahori, K. / Kobayashi, M. / Yamashita, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2za7.cif.gz | 51.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2za7.ent.gz | 38.1 KB | Display | PDB format |
PDBx/mmJSON format | 2za7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2za7_validation.pdf.gz | 350.6 KB | Display | wwPDB validaton report |
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Full document | 2za7_full_validation.pdf.gz | 350.7 KB | Display | |
Data in XML | 2za7_validation.xml.gz | 4.6 KB | Display | |
Data in CIF | 2za7_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/za/2za7 ftp://data.pdbj.org/pub/pdb/validation_reports/za/2za7 | HTTPS FTP |
-Related structure data
Related structure data | 2za6C 2za8C 1aewS 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
#1: Protein | Mass: 19554.100 Da / Num. of mol.: 1 / Fragment: residues 5-175 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Plasmid: PMK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P02791 |
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#2: Water | ChemComp-HOH / |
Sequence details | SEE REF. 2 IN THE DATABASE, P02791 IN UNP. |
-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: 60.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Tris-HCl, 0.13% cadmium chloride, 15% PEG4000, 190mM calcium chloride, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9 Å |
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Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 20, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→41.52 Å / Num. obs: 51287 / Biso Wilson estimate: 13.8 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AEW Resolution: 1.4→41.52 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.923 / SU B: 1.473 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.064 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.713 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→41.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20 /
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