+Open data
-Basic information
Entry | Database: PDB / ID: 1bcf | ||||||
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Title | THE STRUCTURE OF A UNIQUE, TWO-FOLD SYMMETRIC, HAEM-BINDING SITE | ||||||
Components | BACTERIOFERRITIN | ||||||
Keywords | IRON STORAGE AND ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information iron ion sequestering activity / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / oxidoreductase activity / iron ion binding / heme binding / protein homodimerization activity ...iron ion sequestering activity / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / oxidoreductase activity / iron ion binding / heme binding / protein homodimerization activity / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.9 Å | ||||||
Authors | Frolow, F. / Kalb(Gilboa), A.J. / Yariv, J. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1994 Title: Structure of a unique twofold symmetric haem-binding site. Authors: Frolow, F. / Kalb, A.J. / Yariv, J. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1993 Title: Location of Haem in Bacterioferritin of Escherichia Coli Authors: Frolow, F. / Kalb(Gilboa), A.J. / Yariv, J. #2: Journal: Biochem.Biophys.Res.Commun. / Year: 1989 Title: Amino Acid Sequence of the Bacterioferritin (Cytochrome B1) of Escherichia Coli-K12 Authors: Andrews, S.C. / Smith, J.M.A. / Guest, J.R. / Harrison, P.M. #3: Journal: J.Mol.Biol. / Year: 1989 Title: Molecular Size and Symmetry of the Bacterioferritin of Escherichia Coli: X-Ray Crystallographic Characterization of Four Crystal Forms Authors: Smith, J.M.A. / Ford, G.C. / Harrison, P.M. / Yariv, J. / Kalb(Gilboa), A.J. #4: Journal: Biochem.J. / Year: 1983 Title: The Identity of Bacterioferritin and Cytochrome B1 Authors: Yariv, J. #5: Journal: Biochem.J. / Year: 1981 Title: The Composition and the Structure of Bacterioferritin of Escherichia Coli Authors: Yariv, J. / Kalb(Gilboa), A.J. / Sperling, R. / Bauminger, E.R. / Cohen, S.G. / Ofer, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bcf.cif.gz | 377 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bcf.ent.gz | 312.2 KB | Display | PDB format |
PDBx/mmJSON format | 1bcf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/1bcf ftp://data.pdbj.org/pub/pdb/validation_reports/bc/1bcf | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE BACTERIOFERRITIN MOLECULE IS A HOLLOW SHELL OF APPROXIMATE 432 SYMMETRY COMPOSED OF 24 IDENTICAL PROTEIN CHAINS AND 12 HEME GROUPS. THE BUILDING BLOCK FOR THE SHELL IS A PROTEIN DIMER HOLDING THE HEME MOIETY WITH ITS QUASI-DYAD AXIS CLOSELY ALIGNED WITH THE PSEUDO-DYAD OF THE DIMER. A COMPLETE SHELL CAN BE CONSTRUCTED FROM THE COORDINATES GIVEN BELOW FOR PROTEIN SUBUNITS *A* AND *B* AND THE HEME PROSTHETIC GROUP *HEM* BY FIRST APPLYING EACH OF THE FIVE NON-CRYSTALLOGRAPHIC SYMMETRY MATRICES GIVEN BELOW (MTRIX1...MTRIX5) TO OBTAIN ONE ASYMMETRIC UNIT CONSISTING OF ONE HALF OF THE SHELL AND THEN APPLYING THE CRYSTALLOGRAPHIC TWO-FOLD ROTATION (Y, X, -Z) TO THIS. |
-Components
#1: Protein | Mass: 18518.016 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0ABD3 #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-HEM / Compound details | EACH SUBUNIT INCLUDES A BINUCLEAR METAL-BINDING SITE INVOLVING RESIDUES GLU 18, GLU 51, HIS 54, GLU ...EACH SUBUNIT INCLUDES A BINUCLEAR METAL-BINDING SITE INVOLVING RESIDUES GLU 18, GLU 51, HIS 54, GLU 94, GLU 127, AND HIS 130 AND LINKING TOGETHER THE FOUR MAJOR HELICES (A, B, C, AND D) OF THE SUBUNIT. THE IDENTITY OF THE METAL IONS HAS NOT BEEN DETERMINED | Nonpolymer details | THE HEME MOIETY IS BOUND SYMMETRICALLY TO SUBUNITS *A* AND *B* BY BONDS FROM THE HEME IRON TO THE ...THE HEME MOIETY IS BOUND SYMMETRICA | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.2 % | ||||||||||||||||||
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Crystal grow | *PLUS Method: microdialysis / Details: Smith, J.M.A. (1989) J. Mol. Biol., 205, 465. | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.9 Å / Num. obs: 71796 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Num. measured all: 733629 / Rmerge(I) obs: 0.082 |
-Processing
Software |
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Refinement | Resolution: 2.9→8 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 2.9→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 71796 / Rfactor all: 0.208 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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