+Open data
-Basic information
Entry | Database: PDB / ID: 1ier | ||||||
---|---|---|---|---|---|---|---|
Title | CUBIC CRYSTAL STRUCTURE OF NATIVE HORSE SPLEEN FERRITIN | ||||||
Components | FERRITIN | ||||||
Keywords | IRON STORAGE / FERRITIN / APOFERRITIN | ||||||
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 / Resolution: 2.26 Å | ||||||
Authors | Granier, T. / Gallois, B. / Dautant, A. / Langlois D'Estaintot, B. / Precigoux, G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1997 Title: Comparison of the structures of the cubic and tetragonal forms of horse-spleen apoferritin. Authors: Granier, T. / Gallois, B. / Dautant, A. / Langlois d'Estaintot, B. / Precigoux, G. #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: Acta Crystallogr.,Sect.D / Year: 1994 Title: A Crystallographic Study of Haem Binding to Ferritin Authors: Precigoux, G. / Yariv, J. / Gallois, B. / Dautant, A. / Courseille, C. / Langlois D'Estaintot, B. #3: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ier.cif.gz | 50.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ier.ent.gz | 38.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ier.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ier_validation.pdf.gz | 367 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ier_full_validation.pdf.gz | 372.6 KB | Display | |
Data in XML | 1ier_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | 1ier_validation.cif.gz | 8.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/1ier ftp://data.pdbj.org/pub/pdb/validation_reports/ie/1ier | HTTPS FTP |
-Related structure data
Related structure data | 1iesC 1hrsS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| x 24||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 19872.428 Da / Num. of mol.: 1 / Fragment: L-CHAIN / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Organ: SPLEEN / Tissue: SPLEEN / References: UniProt: P02791 | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.7 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.901 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.901 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→19.96 Å / Num. obs: 12699 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 7 % / Rsym value: 0.11 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.26→2.38 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.414 / % possible all: 99.7 |
Reflection | *PLUS Highest resolution: 2.25 Å / Num. measured all: 88762 / Rmerge(I) obs: 0.11 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: 1HRS Resolution: 2.26→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 2 Details: THE THREE C-TERMINAL RESIDUES 172 - 174, SIDE CHAIN ATOMS FOR RESIDUES SER 1, GLU 45, GLU 53, GLU 56, GLU 57, ARG 64, LYS 67, SER 131, GLU 136, SER 157 AND GLN 158 ARE POORLY DEFINED IN THE ...Details: THE THREE C-TERMINAL RESIDUES 172 - 174, SIDE CHAIN ATOMS FOR RESIDUES SER 1, GLU 45, GLU 53, GLU 56, GLU 57, ARG 64, LYS 67, SER 131, GLU 136, SER 157 AND GLN 158 ARE POORLY DEFINED IN THE ELECTRON DENSITY MAP, PROBABLY BECAUSE OF DISORDER. ALL THE REMAINING RESIDUES HAVE WELL DEFINED DENSITY.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.26→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.26→2.31 Å / Total num. of bins used: 15
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 2.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.186 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|