+Open data
-Basic information
Entry | Database: PDB / ID: 2g4h | ||||||
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Title | Anomalous substructure of apoferritin | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL BINDING PROTEIN / anomalous substructure of 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 / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Mueller-Dieckmann, C. / Weiss, M.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths. Authors: Mueller-Dieckmann, C. / Panjikar, S. / Schmidt, A. / Mueller, S. / Kuper, J. / Geerlof, A. / Wilmanns, M. / Singh, R.K. / Tucker, P.A. / Weiss, M.S. | ||||||
History |
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Remark 300 | BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICALLY SIGNIFICANT MOLECULE IS A HOLLOW, SPHERICAL SHELL MADE OF 24 PROTEIN CHAINS ARRANGED IN A 4 3 2 POINT SYMMETRY. A COMPLETE 24-MER (CENTERED AT X = 0, Y = 0, Z = 0) CAN BE GENERATED BY APPLYING THE 24 NON TRANSLATIONAL SYMMETRY OPERATIONS OF THE F 4 3 2 SPACE GROUP TO THE ASYMMETRICAL SUBUNIT BELOW. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g4h.cif.gz | 51.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g4h.ent.gz | 38.2 KB | Display | PDB format |
PDBx/mmJSON format | 2g4h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g4h_validation.pdf.gz | 418.5 KB | Display | wwPDB validaton report |
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Full document | 2g4h_full_validation.pdf.gz | 419.4 KB | Display | |
Data in XML | 2g4h_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 2g4h_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/2g4h ftp://data.pdbj.org/pub/pdb/validation_reports/g4/2g4h | HTTPS FTP |
-Related structure data
Related structure data | 2g4iC 2g4jC 2g4kC 2g4lC 2g4mC 2g4nC 2g4oC 2g4pC 2g4qC 2g4rC 2g4sC 2g4tC 2g4uC 2g4vC 2g4wC 2g4xC 2g4yC 2g4zC 2g51C 2g52C 2g55C 2illC 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: 19856.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P02791 | ||||
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#2: Chemical | ChemComp-CD / #3: Chemical | #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: 3.17 Å3/Da / Density % sol: 61.2 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 2 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 18033 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.694 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.213 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.053 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 0 Å / Origin y: 0 Å / Origin z: 0 Å
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