- PDB-3i92: Structure of the cytosolic domain of E. coli FeoB, GppCH2p-bound form -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3i92
Title
Structure of the cytosolic domain of E. coli FeoB, GppCH2p-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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.1 Å3/Da / Density % sol: 41.53 %
Crystal grow
Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 30% PEG 3350, 12.5% tacsimate, 250 mM 6-amino hexanoic acid, 100 mM HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K
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Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04 Å
Detector
Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 11, 2007
Radiation
Monochromator: bent Si (111) crystal, horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.04 Å / Relative weight: 1
Reflection
Resolution: 3→45.45 Å / Num. obs: 14810
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Processing
Software
Name
Version
Classification
ProDC
datacollection
PHASER
phasing
REFMAC
5.3.0037
refinement
MOSFLM
datareduction
SCALA
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→45.45 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.831 / Cross valid method: THROUGHOUT / ESU R Free: 0.553 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2718
745
5 %
RANDOM
Rwork
0.21658
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obs
0.21942
14055
96.62 %
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all
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14055
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 25.133 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.02 Å2
0 Å2
-0.01 Å2
2-
-
-0.03 Å2
0 Å2
3-
-
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0.01 Å2
Refinement step
Cycle: LAST / Resolution: 3→45.45 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5994
0
99
16
6109
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.006
0.022
6176
X-RAY DIFFRACTION
r_bond_other_d
0
0.02
4058
X-RAY DIFFRACTION
r_angle_refined_deg
1.015
1.999
8410
X-RAY DIFFRACTION
r_angle_other_deg
4.256
3
9962
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.02
5
774
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.976
24.778
270
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.024
15
1076
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.655
15
45
X-RAY DIFFRACTION
r_chiral_restr
0.05
0.2
999
X-RAY DIFFRACTION
r_gen_planes_refined
0.002
0.02
6792
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
1131
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.127
0.2
133
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
0.133
0.2
51
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.174
0.2
131
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.199
0.2
7
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
0.199
1.5
3865
X-RAY DIFFRACTION
r_mcbond_other
0
1.5
1574
X-RAY DIFFRACTION
r_mcangle_it
0.364
2
6220
X-RAY DIFFRACTION
r_scbond_it
0.405
3
2311
X-RAY DIFFRACTION
r_scangle_it
0.679
4.5
2190
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 3→3.078 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.408
45
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Rwork
0.286
1044
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obs
-
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97.84 %
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