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- PDB-4xku: E coli BFR variant Y114F -

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Basic information

Entry
Database: PDB / ID: 4xku
TitleE coli BFR variant Y114F
ComponentsBacterioferritin
KeywordsMETAL BINDING PROTEIN / Iron Storage / diiron site
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsHemmings, A.M. / Le Brun, N.E. / Bradley, J.M.
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.auth_seq_id / _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)223,46527
Polymers222,02412
Non-polymers1,44115
Water53,8112987
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)446,93054
Polymers444,04824
Non-polymers2,88230
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_776-y+2,-x+2,-z+11
Buried area80260 Å2
ΔGint-698 kcal/mol
Surface area132980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.560, 207.560, 142.590
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-502-

HOH

21E-376-

HOH

31E-459-

HOH

41L-394-

HOH

51L-440-

HOH

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Components

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


Mass: 18502.016 Da / Num. of mol.: 12 / Mutation: Y114F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: bfr, b3336, JW3298 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABD3, ferroxidase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2987 / 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: 3.46 Å3/Da / Density % sol: 64.44 %
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: I04-1 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.78→102.271 Å / Num. obs: 287797 / % possible obs: 96.5 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.6
Reflection shellResolution: 1.78→1.83 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2.5 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
xia2data reduction
PHENIX(phenix.phaser-MR: 1.8.2_1309)phasing
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y3Q

2y3q


Resolution: 1.78→102.271 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2169 14123 5.01 %
Rwork0.1879 --
obs0.1894 282002 95.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→102.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15448 0 75 2987 18510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00616380
X-RAY DIFFRACTIONf_angle_d0.92122205
X-RAY DIFFRACTIONf_dihedral_angle_d13.8366385
X-RAY DIFFRACTIONf_chiral_restr0.0672392
X-RAY DIFFRACTIONf_plane_restr0.0032943
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.80020.30614840.28819083X-RAY DIFFRACTION98
1.8002-1.82140.32494760.28019040X-RAY DIFFRACTION98
1.8214-1.84360.30444550.26599065X-RAY DIFFRACTION98
1.8436-1.8670.3124440.26679037X-RAY DIFFRACTION97
1.867-1.89150.29564460.24928714X-RAY DIFFRACTION95
1.8915-1.91750.28574520.23788975X-RAY DIFFRACTION97
1.9175-1.94480.26655020.22319003X-RAY DIFFRACTION98
1.9448-1.97390.26744930.21189052X-RAY DIFFRACTION98
1.9739-2.00470.2284810.20719006X-RAY DIFFRACTION98
2.0047-2.03760.22544370.21169046X-RAY DIFFRACTION97
2.0376-2.07270.23414570.20279007X-RAY DIFFRACTION98
2.0727-2.11040.22684620.19899055X-RAY DIFFRACTION98
2.1104-2.1510.21914810.18358958X-RAY DIFFRACTION97
2.151-2.19490.214590.1789010X-RAY DIFFRACTION97
2.1949-2.24270.21994430.17669036X-RAY DIFFRACTION97
2.2427-2.29480.20954730.17018971X-RAY DIFFRACTION97
2.2948-2.35220.21194780.18068809X-RAY DIFFRACTION95
2.3522-2.41580.20214540.17448730X-RAY DIFFRACTION94
2.4158-2.48690.21064940.17658945X-RAY DIFFRACTION97
2.4869-2.56720.20985050.17348906X-RAY DIFFRACTION96
2.5672-2.6590.21155010.18058928X-RAY DIFFRACTION96
2.659-2.76540.19725070.17828931X-RAY DIFFRACTION96
2.7654-2.89130.20414510.1718941X-RAY DIFFRACTION96
2.8913-3.04370.20964730.16858890X-RAY DIFFRACTION95
3.0437-3.23450.1934620.1718828X-RAY DIFFRACTION94
3.2345-3.48420.1974360.16198645X-RAY DIFFRACTION92
3.4842-3.83480.18094950.15798859X-RAY DIFFRACTION94
3.8348-4.38980.16764850.15228836X-RAY DIFFRACTION94
4.3898-5.53060.20724500.18248881X-RAY DIFFRACTION93
5.5306-102.44040.23134870.22668692X-RAY DIFFRACTION88

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