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- PDB-1bfr: IRON STORAGE AND ELECTRON TRANSPORT -

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Basic information

Entry
Database: PDB / ID: 1bfr
TitleIRON STORAGE AND ELECTRON TRANSPORT
ComponentsBACTERIOFERRITIN
KeywordsELECTRON TRANSPORT / IRON STORAGE
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: 2.94 Å
AuthorsDautant, A. / Yariv, J. / Meyer, J.B. / Precigoux, G. / Sweet, R.M. / Frolow, F. / Kalb(Gilboa), A.J.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure of a monoclinic crystal from of cyctochrome b1 (Bacterioferritin) from E. coli.
Authors: Dautant, A. / Meyer, J.B. / Yariv, J. / Precigoux, G. / Sweet, R.M. / Kalb, A.J. / Frolow, F.
#1: Journal: Nat.Struct.Biol. / Year: 1994
Title: Structure of a Unique Twofold Symmetric Haem-Binding Site
Authors: Frolow, F. / Kalb, A.J. / Yariv, J.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: A Crystallographic Study of Haem Binding to Ferritin
Authors: Precigoux, G. / Yariv, J. / Gallois, B. / Dautant, A. / Courseille, C. / Langlois D'Estaintot, B.
#3: 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. / Guest, J.R. / Harrison, P.M.
#4: 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. / Ford, G.C. / Harrison, P.M. / Yariv, J. / Kalb, A.J.
#5: Journal: Biochem.J. / Year: 1983
Title: The Identity of Bacterioferritin and Cytochrome B1
Authors: Yariv, J.
History
DepositionDec 16, 1994Processing site: BNL
Revision 1.0Jun 20, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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_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_asym_id / _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
M: BACTERIOFERRITIN
N: BACTERIOFERRITIN
O: BACTERIOFERRITIN
P: BACTERIOFERRITIN
Q: BACTERIOFERRITIN
R: BACTERIOFERRITIN
S: BACTERIOFERRITIN
T: BACTERIOFERRITIN
U: BACTERIOFERRITIN
V: BACTERIOFERRITIN
W: BACTERIOFERRITIN
X: BACTERIOFERRITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)454,46784
Polymers444,43224
Non-polymers10,03560
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area91010 Å2
ΔGint-672 kcal/mol
Surface area131390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.700, 211.600, 123.300
Angle α, β, γ (deg.)90.00, 119.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.915893, -0.174434, 0.361541), (-0.353332, 0.077137, 0.932313), (-0.190516, -0.981643, 0.009017)-5.6894, -12.4003, 22.7255
2given(0.832001, -0.527363, 0.17223), (-0.527301, -0.84821, -0.04993), (0.172418, -0.049275, -0.983791)-0.5683, 10.0312, 36.2319
3given(0.91628, -0.352022, -0.191078), (-0.176033, 0.074592, -0.981554), (0.359782, 0.933015, 0.006379)5.1988, 22.4169, 13.5283
4given(-0.280314, -0.959895, -0.005009), (0.366856, -0.102307, -0.924635), (0.88704, -0.261026, 0.380821)43.4996, -0.7404, -22.1888
5given(-0.273367, -0.791505, 0.546617), (-0.208576, 0.603517, 0.769586), (-0.939024, 0.096368, -0.330071)32.5157, -11.1423, 65.4919
6given(-0.999984, -0.001544, -0.005366), (-0.001771, -0.823701, 0.567022), (-0.005296, 0.567023, 0.823685)77.2662, -23.3118, 7.4626
7given(-0.914359, 0.180473, -0.362461), (0.17993, -0.62083, -0.763017), (-0.36273, -0.762889, 0.535189)82.8019, -0.2093, 19.2127
8given(-0.831784, 0.530234, -0.164277), (0.529807, 0.670009, -0.519993), (-0.165651, -0.519556, -0.838225)77.5552, -10.9079, 43.0037
9given(-0.917938, 0.345687, 0.194656), (0.348382, 0.467657, 0.812359), (0.18979, 0.813509, -0.549711)71.9054, -34.1257, 31.2201
10given(0.275249, 0.961372, 0.001633), (0.203353, -0.059882, 0.977273), (0.93962, -0.268661, -0.21198)34.1261, -35.5292, -11.3979
11given(0.280839, 0.788708, -0.546872), (-0.361262, -0.441025, -0.821576), (-0.889168, 0.428295, 0.161073)44.4314, 22.9535, 54.9073

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Components

#1: Protein ...
BACTERIOFERRITIN / / CYTOCHROME B


Mass: 18518.016 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ABD3
#2: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 12 / 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 201, 202).
Nonpolymer detailsHEM IS POSITIONED BETWEEN TWO SUBUNITS WITH ITS QUASI TWO-FOLD AXIS NEARLY COINCIDING WITH A NON- ...HEM IS POSITIONED BETWEEN TWO SUBUNITS WITH ITS QUASI TWO-FOLD AXIS NEARLY COINCIDING WITH A NON-CRYSTALLOGRAPHIC AXIS RELATING THE TWO SUBUNITS. AT THE RESOLUTION OF THE PRESENT DATA, IT IS NOT POSSIBLE TO DETERMINE WHETHER HAEM IS BOUND IN ONE ORIENTATION ONLY OR IN THE TWO TWO-FOLD SYMMETRY RELATED ORIENTATIONS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.59 %
Crystal growDetails: THIS MONOCLINIC CRYSTAL WAS GROWN FROM A SOLUTION OF THE PROTEIN IN DISTILLED WATER BY THE ADDITION OF MN*CL2.
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
22 Mammonium sulfate12
30.1 M12Mn2+
111MnCl2

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.94 Å / Lowest resolution: 46.7 Å / Num. obs: 94076 / Rmerge(I) obs: 0.12

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.94→10 Å / σ(F): 2
Details: THE STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT (PROGRAM *AMORE*) STARTING FROM THE COORDINATES IN PROTEIN DATA BANK ENTRY 1BCF OF BACTERIOFERRITIN IN HIGH SALT AND THE TETRAGONAL CRYSTAL ...Details: THE STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT (PROGRAM *AMORE*) STARTING FROM THE COORDINATES IN PROTEIN DATA BANK ENTRY 1BCF OF BACTERIOFERRITIN IN HIGH SALT AND THE TETRAGONAL CRYSTAL FORM. THE 11 NON-CRYSTALLOGRAPHIC TRANSFORMATIONS GIVEN IN THE *MTRIX* RECORDS WERE USED TO GENERATE THE COMPLETE ASYMMETRIC UNIT PRESENTED IN THIS ENTRY FROM THE COORDINATES PROVIDED BY THE DEPOSITORS. THE ASYMMETRIC UNIT CORRESPONDS TO 24 SUBUNITS AND 12 HEME MOLECULES AND THIS REPRESENTS A MOLECULE OF BACTERIOFERRITIN. STRONG ELECTRON DENSITY WAS OBSERVED ON THE FOUR-FOLD AXIS AT (X = 38.333, Y = 8.691, Z = 69.167). NO ATOM IS ASSIGNED TO THIS DENSITY UNTIL FURTHER EVIDENCE IS OBTAINED.
RfactorNum. reflection% reflection
Rwork0.216 --
obs0.216 91768 83.6 %
Refinement stepCycle: LAST / Resolution: 2.94→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31176 0 564 0 31740
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg2.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refinement
*PLUS
Num. reflection obs: 91554 / Rfactor obs: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 11 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg2.3
X-RAY DIFFRACTIONx_dihedral_angle_deg19
X-RAY DIFFRACTIONx_improper_angle_deg1.7

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