+Open data
-Basic information
Entry | Database: PDB / ID: 6ra8 | ||||||
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Title | Horse spleen apoferritin under 2 kBar of argon | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL TRANSPORT / apoferritin horse spleen argon pressure | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Prange, T. / Carpentier, P. / Colloc'h, N. | ||||||
Citation | Journal: To be published Title: Labelling protein crystals by argon at 2 kbar Authors: Prange, T. / Carpentier, P. #1: Journal: Journal of Applied Crystallography / Year: 2016 Title: Gas-sensitive biological crystals processed in pressurized oxygen and krypton atmospheres: deciphering gas channels in proteins using a novel soak-and-freeze methodology Authors: Lafumat, B. / Mueller-Dieckmann, C. / Leonard, G. / Colloc'h, N. / Prange, T. / Giraud, T. / Dobias, F. / Royant, A. / van der Linden, P. / Carpentier, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ra8.cif.gz | 57.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ra8.ent.gz | 42 KB | Display | PDB format |
PDBx/mmJSON format | 6ra8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ra/6ra8 ftp://data.pdbj.org/pub/pdb/validation_reports/ra/6ra8 | HTTPS FTP |
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-Related structure data
Related structure data | 6q8rC 6q8sC 6qarC 2w0oS S: Starting model for refinement C: citing same article (ref.) |
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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: 19773.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: CYS 48 residue oxidized in CSO last residue 174 not observed in electron density Source: (natural) Equus caballus (horse) / Organ: Spleen / References: UniProt: P02791 | ||||||
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#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-AR / | #4: Chemical | #5: 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: 3.1 Å3/Da / Density % sol: 60.4 % / Description: diamond yellowish crystals |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Ammonium sulfate 0.6 M + cadmium sulfate 0.1 M |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.771 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2018 / Details: bending mirrot |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.771 Å / Relative weight: 1 |
Reflection | Resolution: 2→45.26 Å / Num. obs: 17689 / % possible obs: 100 % / Redundancy: 67.6 % / Biso Wilson estimate: 30.1 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.012 / Net I/σ(I): 40.1 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 61.9 % / Rmerge(I) obs: 0.679 / Mean I/σ(I) obs: 8 / Num. unique obs: 2516 / CC1/2: 0.978 / Rpim(I) all: 0.086 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2w0o.pdb Resolution: 2→45.26 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.874 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.141
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.46 Å2
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Refinement step | Cycle: 1 / Resolution: 2→45.26 Å
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