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Yorodumi- PDB-1nfv: X-ray structure of Desulfovibrio desulfuricans bacterioferritin: ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nfv | ||||||
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Title | X-ray structure of Desulfovibrio desulfuricans bacterioferritin: the diiron centre in different catalytic states (as-isolated structure) | ||||||
Components | bacterioferritin | ||||||
Keywords | IRON STORAGE/ELECTRON TRANSPORT / bacterioferritin / 24 subunits in the active molecule / diiron centre / haem Fe-coproporphyrin III 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 / MAD / Resolution: 1.95 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 | 1nfv.cif.gz | 627.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nfv.ent.gz | 520.9 KB | Display | PDB format |
PDBx/mmJSON format | 1nfv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nfv_validation.pdf.gz | 5.6 MB | Display | wwPDB validaton report |
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Full document | 1nfv_full_validation.pdf.gz | 5.7 MB | Display | |
Data in XML | 1nfv_validation.xml.gz | 144 KB | Display | |
Data in CIF | 1nfv_validation.cif.gz | 180.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/1nfv ftp://data.pdbj.org/pub/pdb/validation_reports/nf/1nfv | 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 relevant molecule is formed applying the following symmetry operations to chains A, B, G, H, I, J, M and N: -z, 1/2+x, 1/2-y and the combination of the three operations 1/2-z, -x, 1/2+y; z, x, y; x-1, y, z; |
-Components
-Protein , 1 types, 16 molecules ABCDEFGHIJKLMNOP
#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 |
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-Non-polymers , 6 types, 2006 molecules
#2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-FEC / #6: Chemical | ChemComp-3PY / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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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 |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.95→30 Å / Num. all: 271259 / Num. obs: 271259 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 6.4 | ||||||||||||||||||
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.1 / % possible all: 97.6 | ||||||||||||||||||
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 905598 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 97.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: polyalanine model, built from scratch Resolution: 1.95→30 Å / Num. restraintsaints: 327899 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: electron density above diiron site not modelled, seems to be a mixture of states
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Displacement parameters | Biso mean: 31.6 Å2 | |||||||||||||||||||||||||||
Refine analyze | Occupancy sum non hydrogen: 24247.95 | |||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.02 Å /
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 1.9 % | |||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.015 |