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- PDB-7r7b: 1.50 Angstroem Crystal Structure of FeoA from Bacteroides fragilis -

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Basic information

Entry
Database: PDB / ID: 7r7b
Title1.50 Angstroem Crystal Structure of FeoA from Bacteroides fragilis
ComponentsFerrous iron transport protein B
KeywordsMETAL TRANSPORT / Feo / SH3 / membrane transporter
Function / homology
Function and homology information


ferrous iron transmembrane transporter activity / transition metal ion binding / GTP binding / plasma membrane
Similarity search - Function
FeoA domain / Ferrous iron transport protein B, C-terminal / Ferrous iron transport protein B C terminus / FeoB, cytosolic helical domain / FeoB cytosolic helical domain / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain / : / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain profile. ...FeoA domain / Ferrous iron transport protein B, C-terminal / Ferrous iron transport protein B C terminus / FeoB, cytosolic helical domain / FeoB cytosolic helical domain / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain / : / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain profile. / Ferrous iron transporter, core domain / Ferrous iron transporter FeoA domain / FeoA / Nucleoside transporter/FeoB GTPase, Gate domain / Nucleoside recognition / Transcriptional repressor, C-terminal / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHATE ION / Ferrous iron transport protein B
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSestok, A.E. / Smith, A.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE027803 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: A fusion of the Bacteroides fragilis ferrous iron import proteins reveals a role for FeoA in stabilizing GTP-bound FeoB.
Authors: Sestok, A.E. / Brown, J.B. / Obi, J.O. / O'Sullivan, S.M. / Garcin, E.D. / Deredge, D.J. / Smith, A.T.
History
DepositionJun 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferrous iron transport protein B
B: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7236
Polymers17,3492
Non-polymers3744
Water2,702150
1
A: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8613
Polymers8,6741
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8613
Polymers8,6741
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.576, 29.552, 67.430
Angle α, β, γ (deg.)90.000, 128.885, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Ferrous iron transport protein B


Mass: 8674.333 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria)
Gene: feoB, BUN20_04310, DW228_07360, DXB57_02360, EC80_0207810, EE52_0204010, EE52_020515, FOC69_09580, IA74_010110, IB64_011160
Production host: Escherichia coli (E. coli) / References: UniProt: A0A081U6Q6
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.07 Å3/Da / Density % sol: 40.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M di-potassium phosphate, 2.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.5→46.16 Å / Num. obs: 23079 / % possible obs: 99.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 14.65 Å2 / CC1/2: 0.992 / Net I/σ(I): 8.1
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 1138 / CC1/2: 0.529

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2K5L

2k5l


Resolution: 1.5→36.03 Å / SU ML: 0.2059 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8118
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2344 1100 4.77 %
Rwork0.1949 21950 -
obs0.1967 23050 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.89 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1176 0 22 150 1348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071253
X-RAY DIFFRACTIONf_angle_d1.05291670
X-RAY DIFFRACTIONf_chiral_restr0.0563186
X-RAY DIFFRACTIONf_plane_restr0.0047206
X-RAY DIFFRACTIONf_dihedral_angle_d16.3966520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.570.40311480.32042693X-RAY DIFFRACTION97.9
1.57-1.650.31961300.25282694X-RAY DIFFRACTION99.61
1.65-1.750.22121230.22612725X-RAY DIFFRACTION99.75
1.75-1.890.24351350.19972737X-RAY DIFFRACTION99.72
1.89-2.080.23971540.19722717X-RAY DIFFRACTION99.97
2.08-2.380.22181290.1922771X-RAY DIFFRACTION99.97
2.38-30.23561630.19722740X-RAY DIFFRACTION99.93
3-36.030.19741180.16482873X-RAY DIFFRACTION99.9

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