+Open data
-Basic information
Entry | Database: PDB / ID: 2ffx | ||||||
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Title | Structure of Human Ferritin L. Chain | ||||||
Components | ferritin light chain | ||||||
Keywords | METAL BINDING PROTEIN / Human Ferritin Light Chain Perdeuterated Capsid | ||||||
Function / homology | Function and homology information Scavenging by Class A Receptors / intracellular ferritin complex / autolysosome / Golgi Associated Vesicle Biogenesis / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / Iron uptake and transport / azurophil granule lumen / iron ion transport ...Scavenging by Class A Receptors / intracellular ferritin complex / autolysosome / Golgi Associated Vesicle Biogenesis / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / Iron uptake and transport / azurophil granule lumen / iron ion transport / intracellular iron ion homeostasis / iron ion binding / Neutrophil degranulation / extracellular exosome / extracellular region / membrane / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Wang, Z.M. / Li, C. / Ellenburg, M.P. / Soitsman, E.M. / Ruble, J.R. / Wright, B.S. / Ho, J.X. / Carter, D.C. | ||||||
Citation | Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2006 Title: Structure of human ferritin L chain Authors: Wang, Z.M. / Li, C. / Ellenburg, M.P. / Soistman, E.M. / Ruble, J.R. / Wright, B.S. / Ho, J.X. / Carter, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ffx.cif.gz | 53.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ffx.ent.gz | 39.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ffx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/2ffx ftp://data.pdbj.org/pub/pdb/validation_reports/ff/2ffx | HTTPS FTP |
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-Related 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: 19802.396 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: perdeuterated salts and solvent / Gene: FTL / Plasmid: pET 11a-LF / Production host: Escherichia coli (E. coli) / References: UniProt: P02792 | ||||
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#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-SO4 / | #4: 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: 3.66 Å3/Da / Density % sol: 66.44 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion / pH: 5.5 Details: 1.6% Cadmium Sulfate, 0.2M Sodium Acetate, pH 5.5, VAPOR DIFFUSION, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 22, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 23698 / Num. obs: 23698 / % possible obs: 100 % / Redundancy: 5.3 % / Biso Wilson estimate: 19.7 Å2 / Rsym value: 0.1 / Net I/σ(I): 7.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→43.76 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 225145.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.9903 Å2 / ksol: 0.372796 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→43.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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