+Open data
-Basic information
Entry | Database: PDB / ID: 1dat | ||||||
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Title | CUBIC CRYSTAL STRUCTURE RECOMBINANT HORSE L APOFERRITIN | ||||||
Components | L FERRITIN | ||||||
Keywords | IRON STORAGE / APOFERRITIN / LIGHT CHAIN | ||||||
Function / homology | Function and homology information intracellular ferritin complex / 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 / Resolution: 2.05 Å | ||||||
Authors | Gallois, B. / Granier, T. / Langlois D'Estaintot, B. / Crichton, R.R. / Roland, F. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 1997 Title: X-ray structure of recombinant horse L-chain apoferritin at 2.0 angstrom resolution: Implications for stability and function. Authors: Gallois, B. / dEstaintot, B.L. / Michaux, M.A. / Dautant, A. / Granier, T. / Precigoux, G. / Soruco, J.A. / Roland, F. / ChavasAlba, O. / Herbas, A. / Crichton, R.R. #1: Journal: Proteins / Year: 1996 Title: Structural Investigation of the Complexation Properties between Horse Spleen Apoferritin and Metalloporphyrins Authors: Michaux, M.A. / Dautant, A. / Gallois, B. / Granier, T. / D'Estaintot, B.L. / Precigoux, G. #2: Journal: Biochim.Biophys.Acta / Year: 1993 Title: Cloning, Expression and Characterization of Horse L-Ferritin in Escherichia Coli Authors: Takeda, S. / Ohta, M. / Ebina, S. / Nagayama, K. #3: Journal: FEBS Lett. / Year: 1981 Title: Amino Acid Sequence of Horse Spleen Apoferritin Authors: Heusterspreute, M. / Crichton, R.R. #4: Journal: Nature / Year: 1980 Title: Helix Packing and Subunit Conformation in Horse Spleen Apoferritin Authors: Clegg, G.A. / Stansfield, R.F. / Bourne, P.E. / Harrison, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dat.cif.gz | 47.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dat.ent.gz | 37.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dat.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/1dat ftp://data.pdbj.org/pub/pdb/validation_reports/da/1dat | HTTPS FTP |
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-Related structure data
Related structure data | 1ierS 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: 19856.385 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Gene: CDNA / Organ: LIVER / Plasmid: BMH-71-18 / Gene (production host): CDNA / Production host: Escherichia coli (E. coli) / References: UniProt: P02791 | ||
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#2: Chemical | #3: 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: 3.26 Å3/Da / Density % sol: 62.2 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.375 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 2, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.375 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→16.05 Å / Num. obs: 16993 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 10.6 % / Biso Wilson estimate: 15.2 Å2 / Rsym value: 0.096 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.05→2.17 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.278 / % possible all: 99.6 |
Reflection | *PLUS Num. obs: 16931 / Num. measured all: 179720 / Rmerge(I) obs: 0.096 |
Reflection shell | *PLUS % possible obs: 99.6 % / Rmerge(I) obs: 0.278 |
-Processing
Software |
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Refinement | Starting model: PDB ENTRY 1IER Resolution: 2.05→8 Å / σ(F): 4
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Displacement parameters | Biso mean: 19.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.15 Å
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Software | *PLUS Name: X-PLOR / Version: 2.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.179 / Rfactor Rwork: 0.179 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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