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Yorodumi- PDB-1nf4: X-Ray Structure of the Desulfovibrio desulfuricans bacterioferrit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nf4 | ||||||
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Title | X-Ray Structure of the Desulfovibrio desulfuricans bacterioferritin: the diiron site in different states (reduced structure) | ||||||
Components | bacterioferritin | ||||||
Keywords | IRON STORAGE/ELECTRON TRANSPORT / bacterioferritin / active as 24-mer / diiron centre / Fe-coproporphyrin III haem cofactor / IRON STORAGE-ELECTRON TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / heme binding / cytosol Similarity search - Function | ||||||
Biological species | Desulfovibrio desulfuricans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / structure solved using the native as-isolated structure as starting model / Resolution: 2.05 Å | ||||||
Authors | Macedo, S. / Romao, C.V. / Mitchell, E. / Matias, P.M. / Liu, M.Y. / Xavier, A.V. / LeGall, J. / Teixeira, M. / Lindley, P. / Carrondo, M.A. | ||||||
Citation | Journal: NAT.STRUCT.BIOL. / Year: 2003 Title: The nature of the di-iron site in the bacterioferritin from Desulfovibrio desulfuricans Authors: Macedo, S. / Romao, C.V. / Mitchell, E. / Matias, P.M. / Liu, M.Y. / Xavier, A.V. / LeGall, J. / Teixeira, M. / Lindley, P. / Carrondo, M.A. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Structure determination of bacterioferritin from Desulfovibrio desulfuricans by the MAD method at the Fe K-edge Authors: Coelho, A.V. / Macedo, S. / Matias, P.M. / Thompson, A.W. / LeGall, J. / Carrondo, M.A. | ||||||
History |
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Remark 350 | GENERATING THE BIOMOLECULE THE ACTIVE BIOLOGICAL UNIT IS A 24-MER. SINCE THE ASYMMETRIC UNIT ...GENERATING THE BIOMOLECULE THE ACTIVE BIOLOGICAL UNIT IS A 24-MER. SINCE THE ASYMMETRIC UNIT CONTAINS PARTS OF TWO DIFFERENT SPHERES, APPLY THE SYMMETRY OPERATIONS (-z, 1/2+x, 1/2-y) AND (y-1/2, 1/2-z, -x) TO MONOMERS A, B, G, H, I, J, M AND N OR THE SYMMETRY OPERATIONS (z+1/2, 1/2-x, -y) AND (1/2-y, -z, x-1/2) TO THE REMAINING MONOMERS IN THE ASYMMETRIC UNIT TO GENERATE THE 24-MER. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nf4.cif.gz | 598.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nf4.ent.gz | 495.1 KB | Display | PDB format |
PDBx/mmJSON format | 1nf4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nf4_validation.pdf.gz | 5.5 MB | Display | wwPDB validaton report |
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Full document | 1nf4_full_validation.pdf.gz | 5.6 MB | Display | |
Data in XML | 1nf4_validation.xml.gz | 132.4 KB | Display | |
Data in CIF | 1nf4_validation.cif.gz | 168.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/1nf4 ftp://data.pdbj.org/pub/pdb/validation_reports/nf/1nf4 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Details | the biologically active 24-mer is formed applying the following operations to monomers A, B, G, H, I, J, M N: -z, 1/2+x, 1/2-y and combination of the three operations 1/2-z, -x, 1/2+y z, x, y x-1, y,z |
-Components
#1: Protein | Mass: 19906.281 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio desulfuricans (bacteria) / Strain: ATCC 27774 / References: GenBank: 14326006, UniProt: Q93PP9*PLUS #2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-FEC / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: ammonium sulfate, sodium acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 3.6 Details: Coelho, A.V., (2001) Acta Crystallogr., Sect.D, 57, 326. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 6, 2000 / Details: toroidal mirrors |
Radiation | Monochromator: diamond (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30 Å / Num. all: 234647 / Num. obs: 234647 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 2.4 / Num. unique all: 23163 / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 99 % / Num. measured all: 871754 |
Reflection shell | *PLUS % possible obs: 99.8 % |
-Processing
Software |
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Refinement | Method to determine structure: structure solved using the native as-isolated structure as starting model Starting model: as-isolated native model obtained for the same protein by the MAD method Resolution: 2.05→30 Å / Num. restraintsaints: 361965 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 31.6 Å2 | |||||||||||||||||||||||||
Refine analyze | Occupancy sum non hydrogen: 23787.42 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.13 Å /
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Refinement | *PLUS Lowest resolution: 30 Å / Rfactor Rfree: 0.27 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Lowest resolution: 2.12 Å / Rfactor Rfree: 0.021 |