- PDB-3i8x: Structure of the cytosolic domain of E. coli FeoB, GDP-bound form -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3i8x
Title
Structure of the cytosolic domain of E. coli FeoB, GDP-bound form
Components
Ferrous iron transport protein B
Keywords
TRANSPORT PROTEIN / GTPase / GPCR / iron uptake / Feo / Cell inner membrane / Cell membrane / GTP-binding / Ion transport / Iron / Iron transport / Membrane / Nucleotide-binding / Transmembrane / Transport
Function / homology
Function and homology information
iron ion import across plasma membrane / ferrous iron transmembrane transporter activity / DNA damage response / GTP binding / identical protein binding / plasma membrane Similarity search - Function
Helix Hairpins - #1770 / FeoB, cytosolic helical domain / FeoB cytosolic helical domain / Ferrous iron transport protein B, C-terminal / Ferrous iron transport protein B C terminus / 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. / Nucleoside transporter/FeoB GTPase, Gate domain ...Helix Hairpins - #1770 / FeoB, cytosolic helical domain / FeoB cytosolic helical domain / Ferrous iron transport protein B, C-terminal / Ferrous iron transport protein B C terminus / 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. / Nucleoside transporter/FeoB GTPase, Gate domain / Nucleoside recognition / Helix Hairpins / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
Resolution: 2.25→25.14 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.902 / SU B: 7.573 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.373 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24965
1798
5 %
RANDOM
Rwork
0.18622
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-
-
obs
0.18946
34179
99.99 %
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all
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34179
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-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 21.955 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.03 Å2
0 Å2
0.02 Å2
2-
-
-0.04 Å2
0 Å2
3-
-
-
0.01 Å2
Refinement step
Cycle: LAST / Resolution: 2.25→25.14 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6045
0
84
315
6444
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
6223
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
4100
X-RAY DIFFRACTION
r_angle_refined_deg
1.516
1.996
8479
X-RAY DIFFRACTION
r_angle_other_deg
0.963
3
10074
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.431
5
792
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.197
24.743
272
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.83
15
1093
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.024
15
46
X-RAY DIFFRACTION
r_chiral_restr
0.076
0.2
1009
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
6878
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
1146
X-RAY DIFFRACTION
r_nbd_refined
0.207
0.2
1244
X-RAY DIFFRACTION
r_nbd_other
0.192
0.2
4169
X-RAY DIFFRACTION
r_nbtor_refined
0.166
0.2
2933
X-RAY DIFFRACTION
r_nbtor_other
0.088
0.2
3396
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.18
0.2
287
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.191
0.2
35
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.288
0.2
112
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.201
0.2
19
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.116
1.5
5097
X-RAY DIFFRACTION
r_mcbond_other
0.148
1.5
1587
X-RAY DIFFRACTION
r_mcangle_it
1.293
2
6289
X-RAY DIFFRACTION
r_scbond_it
2.052
3
2629
X-RAY DIFFRACTION
r_scangle_it
3.016
4.5
2183
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.25→2.308 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.374
123
-
Rwork
0.229
2468
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obs
-
-
100 %
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