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- PDB-1bcf: THE STRUCTURE OF A UNIQUE, TWO-FOLD SYMMETRIC, HAEM-BINDING SITE -

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Basic information

Entry
Database: PDB / ID: 1bcf
TitleTHE STRUCTURE OF A UNIQUE, TWO-FOLD SYMMETRIC, HAEM-BINDING SITE
ComponentsBACTERIOFERRITIN
KeywordsIRON STORAGE AND ELECTRON TRANSPORT
Function / homology
Function and homology information


ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / oxidoreductase activity / iron ion binding / heme binding / protein homodimerization activity / membrane ...ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / oxidoreductase activity / iron ion binding / heme binding / protein homodimerization activity / membrane / identical protein binding / cytosol
Similarity search - Function
Bacterioferritin signature. / Bacterioferritin / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...Bacterioferritin signature. / Bacterioferritin / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / : / Bacterioferritin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsFrolow, 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
DepositionDec 6, 1993Processing site: BNL
Revision 1.0Dec 20, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BACTERIOFERRITIN
B: BACTERIOFERRITIN
C: BACTERIOFERRITIN
D: BACTERIOFERRITIN
E: BACTERIOFERRITIN
F: BACTERIOFERRITIN
G: BACTERIOFERRITIN
H: BACTERIOFERRITIN
I: BACTERIOFERRITIN
J: BACTERIOFERRITIN
K: BACTERIOFERRITIN
L: BACTERIOFERRITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,23442
Polymers222,21612
Non-polymers5,01730
Water0
1
A: BACTERIOFERRITIN
B: BACTERIOFERRITIN
C: BACTERIOFERRITIN
D: BACTERIOFERRITIN
E: BACTERIOFERRITIN
F: BACTERIOFERRITIN
G: BACTERIOFERRITIN
H: BACTERIOFERRITIN
I: BACTERIOFERRITIN
J: BACTERIOFERRITIN
K: BACTERIOFERRITIN
L: BACTERIOFERRITIN
hetero molecules

A: BACTERIOFERRITIN
B: BACTERIOFERRITIN
C: BACTERIOFERRITIN
D: BACTERIOFERRITIN
E: BACTERIOFERRITIN
F: BACTERIOFERRITIN
G: BACTERIOFERRITIN
H: BACTERIOFERRITIN
I: BACTERIOFERRITIN
J: BACTERIOFERRITIN
K: BACTERIOFERRITIN
L: BACTERIOFERRITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)454,46784
Polymers444,43224
Non-polymers10,03560
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area95000 Å2
ΔGint-770 kcal/mol
Surface area133430 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)211.100, 211.100, 145.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.001709, -0.999998, 0.000504), (0.999769, -0.001719, -0.021446), (0.021447, 0.000467, 0.99977)108.44, 0.78, -1.62
2given(-0.999755, -0.005759, 0.02138), (0.005693, -0.999979, -0.00314), (0.021397, -0.003018, 0.999766)108.18, 107.78, -1.66
3given(-0.009622, 0.999952, -0.001574), (-0.999915, -0.009608, 0.008862), (0.008846, 0.001659, 0.999959)1.14, 108.59, -0.96
4given(0.490879, 0.502495, -0.711714), (-0.502123, -0.504412, -0.702453), (-0.711976, 0.702188, 0.004709)0.74, 108.57, 0.53
5given(-0.487883, -0.500876, 0.714908), (0.516301, 0.494795, 0.699007), (-0.703849, 0.710142, 0.017201)107.11, -0.74, -0.78
DetailsTHE 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.

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Components

#1: Protein
BACTERIOFERRITIN /


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 / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
Compound detailsEACH 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. THEY ARE LISTED BELOW AS DIVALENT MANGANESE (RESIDUES *A* 600, *A* 601, *B* 600, AND *B* 601) AND ARE NAMED SITES MA1, MA2, MB1, AND MB2.
Nonpolymer detailsTHE HEME MOIETY IS BOUND SYMMETRICALLY TO SUBUNITS *A* AND *B* BY BONDS FROM THE HEME IRON TO THE ...THE HEME MOIETY IS BOUND SYMMETRICALLY TO SUBUNITS *A* AND *B* BY BONDS FROM THE HEME IRON TO THE SULFUR ATOMS OF MET *A* 52 AND MET *B* 52.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.2 %
Crystal grow
*PLUS
Method: microdialysis / Details: Smith, J.M.A. (1989) J. Mol. Biol., 205, 465.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 Mammonium sulfate11
20.1 M11Mn2+

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative 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

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.9→8 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.208 -
obs0.208 71796
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15564 0 282 0 15846
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.81
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.63
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
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
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d1.81
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg1.63

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