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- PDB-4xkt: E coli BFR variant Y149F -

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Basic information

Entry
Database: PDB / ID: 4xkt
TitleE coli BFR variant Y149F
ComponentsBacterioferritin
KeywordsMETAL BINDING PROTEIN / iron storage / diiron site
Function / homology
Function and homology information


: / iron ion sequestering activity / ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / oxidoreductase activity / iron ion binding / heme binding ...: / iron ion sequestering activity / ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / 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
Bacterioferritin / Bacterioferritin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsBradley, J.M. / Hemmings, A.M. / Le Brun, N.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/IO21884/1 United Kingdom
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Three Aromatic Residues are Required for Electron Transfer during Iron Mineralization in Bacterioferritin.
Authors: Bradley, J.M. / Svistunenko, D.A. / Lawson, T.L. / Hemmings, A.M. / Moore, G.R. / Le Brun, N.E.
History
DepositionJan 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Jan 20, 2016Group: Database references
Revision 2.0Aug 30, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_site_gen.auth_seq_id
Revision 2.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)223,27325
Polymers222,02412
Non-polymers1,24913
Water49,8842769
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)446,54650
Polymers444,04824
Non-polymers2,49826
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_776-y+2,-x+2,-z+11
Buried area30460 Å2
ΔGint-273 kcal/mol
Surface area76780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.470, 208.470, 142.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-399-

HOH

21B-441-

HOH

31G-381-

HOH

41L-442-

HOH

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Components

#1: Protein
Bacterioferritin


Mass: 18502.016 Da / Num. of mol.: 12 / Mutation: Y149F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: bfr, BN1008_2995, BN17_32701, BU34_11470, BU65_02845, BU66_00425, BU67_22375, BU68_21080, BU69_14600, CF57_02675, CF61_03435, DO98_13405, DP79_03550, ECHMS174_03989, ECRV308_03369, EH62_04010, ...Gene: bfr, BN1008_2995, BN17_32701, BU34_11470, BU65_02845, BU66_00425, BU67_22375, BU68_21080, BU69_14600, CF57_02675, CF61_03435, DO98_13405, DP79_03550, ECHMS174_03989, ECRV308_03369, EH62_04010, EH63_09485, EH64_04335, EH65_17065, EH66_25435, EL75_0360, EL77_0399, EL78_0411, EL79_0379, EL80_0371, EP08_09090, GR02_14320, GR05_21335, GR06_21735, KV39_17170, LF82_0224, PGD_00550
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: E2QFJ1, UniProt: P0ABD3*PLUS, ferroxidase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2769 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 1.6M ammonium sulfate 0.1M sodium citrate / PH range: 4.8-5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.82→31.745 Å / Num. obs: 277740 / % possible obs: 99.8 % / Redundancy: 27 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 20.3
Reflection shellResolution: 1.82→1.87 Å / Redundancy: 27.4 % / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 5.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
xia2data reduction
xia2data scaling
PHASER(phenix.phaser-MR: 1.8.2_1309)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2y3q

2y3q


Resolution: 1.82→31.745 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2057 13895 5.02 %Random selection
Rwork0.1672 ---
obs0.1691 276932 99.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.82→31.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15448 0 65 2769 18282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00616966
X-RAY DIFFRACTIONf_angle_d0.84823098
X-RAY DIFFRACTIONf_dihedral_angle_d14.1796690
X-RAY DIFFRACTIONf_chiral_restr0.0652454
X-RAY DIFFRACTIONf_plane_restr0.0023107
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.84070.2714560.19588696X-RAY DIFFRACTION100
1.8407-1.86230.22674730.18628712X-RAY DIFFRACTION100
1.8623-1.8850.25064940.18678658X-RAY DIFFRACTION100
1.885-1.90890.23894600.19328671X-RAY DIFFRACTION100
1.9089-1.9340.25284900.18218693X-RAY DIFFRACTION100
1.934-1.96050.22274370.17138756X-RAY DIFFRACTION100
1.9605-1.98850.2164850.16188656X-RAY DIFFRACTION99
1.9885-2.01820.21994860.16618651X-RAY DIFFRACTION99
2.0182-2.04970.22744750.16578671X-RAY DIFFRACTION99
2.0497-2.08330.2054550.16228719X-RAY DIFFRACTION100
2.0833-2.11920.21855020.15928685X-RAY DIFFRACTION100
2.1192-2.15780.19544620.14828723X-RAY DIFFRACTION100
2.1578-2.19930.18714440.14568766X-RAY DIFFRACTION100
2.1993-2.24410.20654810.15538699X-RAY DIFFRACTION100
2.2441-2.29290.19514590.15028754X-RAY DIFFRACTION100
2.2929-2.34620.20464470.15198793X-RAY DIFFRACTION100
2.3462-2.40490.19494800.15168709X-RAY DIFFRACTION100
2.4049-2.46990.19584530.15368743X-RAY DIFFRACTION100
2.4699-2.54250.19134590.168767X-RAY DIFFRACTION100
2.5425-2.62460.18754250.15758770X-RAY DIFFRACTION99
2.6246-2.71830.21614680.16488789X-RAY DIFFRACTION100
2.7183-2.82710.21254370.16618806X-RAY DIFFRACTION100
2.8271-2.95570.19644290.16388776X-RAY DIFFRACTION99
2.9557-3.11140.19655050.1638793X-RAY DIFFRACTION100
3.1114-3.30610.1834360.15958853X-RAY DIFFRACTION100
3.3061-3.56110.18344540.15378869X-RAY DIFFRACTION99
3.5611-3.91890.19254420.16168863X-RAY DIFFRACTION100
3.9189-4.48460.17414720.15478914X-RAY DIFFRACTION99
4.4846-5.64490.224720.19148971X-RAY DIFFRACTION99
5.6449-31.74930.25394570.24299111X-RAY DIFFRACTION97

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