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Yorodumi- PDB-1lb3: Structure of recombinant mouse L chain ferritin at 1.2 A resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lb3 | ||||||
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Title | Structure of recombinant mouse L chain ferritin at 1.2 A resolution | ||||||
Components | FERRITIN LIGHT CHAIN 1 | ||||||
Keywords | METAL BINDING PROTEIN / IRON STORAGE | ||||||
Function / homology | Function and homology information : / autolysosome / intracellular sequestering of iron ion / endocytic vesicle lumen / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å | ||||||
Authors | Granier, T. / Langlois D'Estaintot, B. / Gallois, B. / Chevalier, J.-M. / Precigoux, G. / Santambrogio, P. / Arosio, P. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2003 Title: Structural description of the active sites of mouse L-chain ferritin at 1.2A resolution Authors: Granier, T. / Langlois D'Estaintot, B. / Gallois, B. / Chevalier, J.-M. / Precigoux, G. / Santambrogio, P. / Arosio, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lb3.cif.gz | 106.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lb3.ent.gz | 80.4 KB | Display | PDB format |
PDBx/mmJSON format | 1lb3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lb3_validation.pdf.gz | 382.4 KB | Display | wwPDB validaton report |
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Full document | 1lb3_full_validation.pdf.gz | 382.6 KB | Display | |
Data in XML | 1lb3_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | 1lb3_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/1lb3 ftp://data.pdbj.org/pub/pdb/validation_reports/lb/1lb3 | HTTPS FTP |
-Related structure data
Related structure data | 1h96S 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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Details | The biological assembly is a 24mer. Coordinates for a complete multimer representing the known biologically significant oligomerization state of the molecule can be generated from the monomer in the assymmetric unit by the following symmetry operations: -X,-Y,Z; -X,Y,-Z; X,-Y,-Z; Z,X,Y; Z,-X,-Y; -Z,-X,Y; -Z,X,-Y; Y,Z,X; -Y,Z,-X; Y,-Z,-X; -Y,-Z,X; Y,X,-Z; -Y,-X,-Z; Y,-X,Z; -Y,X,Z; X,Z,-Y; -X,Z,Y; -X,-Z,-Y; X,-Z,Y; Z,Y,-X; Z,-Y,X; -Z,Y,X; -Z,-Y,-X; |
-Components
#1: Protein | Mass: 20670.164 Da / Num. of mol.: 1 / Mutation: T121A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: FTL / Plasmid: pMLF27 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P29391 | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-CD / #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | CHAIN ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.8 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: ammonium sulphate, cadmium sulphate, sodium azide, tris HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Details: Granier, T., (2001) Acta Crystallogr., D57, 1491. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.966 / Wavelength: 0.966 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 17, 2000 / Details: W/SI MIRRORS |
Radiation | Monochromator: Si (111) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.21→14 Å / Num. all: 74509 / Num. obs: 74509 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rsym value: 0.066 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 1.21→1.25 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2 / Num. unique all: 5144 / Rsym value: 0.48 / % possible all: 98.4 |
Reflection | *PLUS Lowest resolution: 14 Å / Num. measured all: 399787 / Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS % possible obs: 98.4 % / Num. unique obs: 5144 / Rmerge(I) obs: 0.602 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H96 Resolution: 1.21→14 Å / Num. parameters: 16266 / Num. restraintsaints: 16802 / Isotropic thermal model: ANISOTROPIC / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-22 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 38 / Occupancy sum hydrogen: 1287.25 / Occupancy sum non hydrogen: 1622.33 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.21→14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.21→1.26 Å
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 14 Å / Rfactor all: 0.134 / Rfactor Rfree: 0.16 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.22 / Rfactor Rwork: 0.2 |