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- PDB-3e2c: Escherichia coli Bacterioferritin Mutant E128R/E135R -

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Basic information

Entry
Database: PDB / ID: 3e2c
TitleEscherichia coli Bacterioferritin Mutant E128R/E135R
ComponentsBacterioferritin
KeywordsOXIDOREDUCTASE / Diiron site / Iron storage / Metal-binding / Heme / Iron
Function / homology
Function and homology information


iron ion sequestering activity / ferroxidase / ferroxidase activity / intracellular sequestering of iron ion / ferric iron binding / iron ion transport / oxidoreductase activity / iron ion binding / heme binding / protein homodimerization activity ...iron ion sequestering activity / ferroxidase / ferroxidase activity / intracellular sequestering of iron ion / ferric iron binding / iron ion transport / oxidoreductase activity / iron ion binding / heme binding / protein homodimerization activity / identical protein binding / membrane / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsWong, S.G. / Tom-Yew, S.A.L. / Lewin, A. / Le Brun, N.E. / Moore, G.R. / Murphy, M.E.P. / Mauk, A.G.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural and Mechanistic Studies of a Stabilized Subunit Dimer Variant of Escherichia coli Bacterioferritin Identify Residues Required for Core Formation.
Authors: Wong, S.G. / Tom-Yew, S.A. / Lewin, A. / Le Brun, N.E. / Moore, G.R. / Murphy, M.E. / Mauk, A.G.
History
DepositionAug 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: Derived calculations
Revision 1.3Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacterioferritin
B: Bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,95312
Polymers37,1482
Non-polymers1,80410
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-51 kcal/mol
Surface area16970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.639, 91.089, 102.085
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bacterioferritin / BFR / Cytochrome b-1 / Cytochrome b-557


Mass: 18574.176 Da / Num. of mol.: 2 / Mutation: E128R, E135R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: bfr, b3336, JW3298 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0ABD3, ferroxidase

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Non-polymers , 5 types, 238 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.57 %
Crystal growTemperature: 303.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 4000, 0.2M Li2SO4, 0.1M Tris HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 303.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 6, 2006 / Details: mirrors
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 29870 / % possible obs: 99.6 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.048 / Χ2: 1.19
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.866.60.25729110.936198.7
1.86-1.947.20.2229231.006199.9
1.94-2.037.20.14729551.0021100
2.03-2.137.30.10629591.051100
2.13-2.277.30.07729621.0691100
2.27-2.447.30.06129541.0871100
2.44-2.697.20.0529871.1241100
2.69-3.087.20.04630251.3541100
3.08-3.8870.04530412.062199.9
3.88-506.50.02731531.188197.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.54 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1507 5.1 %RANDOM
Rwork0.202 ---
obs0.203 29804 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.35 Å2 / Biso mean: 25.269 Å2 / Biso min: 8.83 Å2
Baniso -1Baniso -2Baniso -3
1-1.74 Å20 Å20 Å2
2---1.27 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2606 0 114 228 2948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212796
X-RAY DIFFRACTIONr_angle_refined_deg1.0632.0723788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5425322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.57124.868152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28215518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4021522
X-RAY DIFFRACTIONr_chiral_restr0.0630.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022140
X-RAY DIFFRACTIONr_nbd_refined0.2170.21468
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21924
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2196
X-RAY DIFFRACTIONr_metal_ion_refined0.1250.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.211
X-RAY DIFFRACTIONr_mcbond_it0.5541.51584
X-RAY DIFFRACTIONr_mcangle_it1.03122533
X-RAY DIFFRACTIONr_scbond_it1.72231212
X-RAY DIFFRACTIONr_scangle_it2.7514.51255
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 122 -
Rwork0.254 1984 -
all-2106 -
obs--97.41 %

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