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- PDB-3iby: Structure of cytosolic domain of L. pneumophila FeoB -

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Basic information

Entry
Database: PDB / ID: 3iby
TitleStructure of cytosolic domain of L. pneumophila FeoB
ComponentsFerrous iron transport protein B
KeywordsTRANSPORT PROTEIN / G protein / G domain / iron uptake / Cell inner membrane / Cell membrane / GTP-binding / Ion transport / Iron / Iron transport / Membrane / Nucleotide-binding / Transmembrane / Transport
Function / homology
Function and homology information


ferrous iron transmembrane transporter activity / GTP binding / plasma membrane
Similarity search - Function
Helix Hairpins - #1770 / 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 - #1770 / 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 / 50S ribosome-binding GTPase / GTP binding domain / 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
Fe(2+) transporter FeoB
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPetermann, N. / Hansen, G. / Hilgenfeld, R.
CitationJournal: Febs Lett. / Year: 2010
Title: Structure of the GTPase and GDI domains of FeoB, the ferrous iron transporter of Legionella pneumophila.
Authors: Petermann, N. / Hansen, G. / Schmidt, C.L. / Hilgenfeld, R.
History
DepositionJul 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Ferrous iron transport protein B
B: Ferrous iron transport protein B
C: Ferrous iron transport protein B
D: Ferrous iron transport protein B


Theoretical massNumber of molelcules
Total (without water)113,6154
Polymers113,6154
Non-polymers00
Water2,108117
1
A: Ferrous iron transport protein B


Theoretical massNumber of molelcules
Total (without water)28,4041
Polymers28,4041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ferrous iron transport protein B


Theoretical massNumber of molelcules
Total (without water)28,4041
Polymers28,4041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ferrous iron transport protein B


Theoretical massNumber of molelcules
Total (without water)28,4041
Polymers28,4041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ferrous iron transport protein B


Theoretical massNumber of molelcules
Total (without water)28,4041
Polymers28,4041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.056, 130.697, 157.616
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Ferrous iron transport protein B


Mass: 28403.684 Da / Num. of mol.: 4 / Fragment: Cytosolic domain (UNP residues 1-256)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: feoB / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(placI) / References: UniProt: Q8GNS3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% tacsimate, 10% poly-L-lysine, 50 mM Hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.75 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 11, 2007
RadiationMonochromator: Double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75 Å / Relative weight: 1
ReflectionResolution: 2.5→78.81 Å / Num. obs: 36133 / % possible obs: 93.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 43.8 Å2 / Rmerge(I) obs: 0.081
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.481 / Num. unique all: 3743 / % possible all: 68.1

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Processing

Software
NameVersionClassification
ProDCdata collection
PHASERphasing
REFMAC5.5.0088refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→78.81 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.89 / SU B: 25.373 / SU ML: 0.25 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.775 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2877 1813 5 %RANDOM
Rwork0.21249 ---
obs0.21621 34319 92.99 %-
all-34319 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.168 Å2
Baniso -1Baniso -2Baniso -3
1--1.93 Å20 Å20 Å2
2--2.1 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.5→78.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7491 0 0 117 7608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0227598
X-RAY DIFFRACTIONr_bond_other_d0.0010.024990
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.97610293
X-RAY DIFFRACTIONr_angle_other_deg0.946312361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3245950
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.04925.964332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.597151399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5011524
X-RAY DIFFRACTIONr_chiral_restr0.0820.21238
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028308
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021324
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5511.54767
X-RAY DIFFRACTIONr_mcbond_other0.1211.51942
X-RAY DIFFRACTIONr_mcangle_it1.02827701
X-RAY DIFFRACTIONr_scbond_it1.7832831
X-RAY DIFFRACTIONr_scangle_it2.8794.52592
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 98 -
Rwork0.267 1712 -
obs--63.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1466-0.1758-1.38593.42051.76381.4898-0.02510.02840.23430.02760.0550.02090.00950.0211-0.02990.0501-0.0086-0.01370.04450.02350.093411.675312.5836-53.734
26.12730.64790.41992.06090.84791.6897-0.0080.1253-0.23160.0520.06230.13210.16380.1393-0.05430.14380.0347-0.00740.0189-0.02090.08787.09810.1899-57.7652
32.0191-1.86770.43382.57161.02513.112-0.1708-0.0891-0.21250.35140.17910.13370.37590.7006-0.00830.1940.04040.03220.5152-0.01330.405424.0982-6.6269-66.5425
410.69475.1321-8.14714.3629-3.57079.739-0.03840.7122-0.2509-0.15280.0408-0.1122-0.01490.1391-0.00240.28220.0504-0.0630.2563-0.05180.23214.907-5.5525-74.8895
51.90290.60361.72613.910.07491.63730.1218-0.0141-0.1470.0097-0.028-0.01080.11860.0162-0.09380.07390.00210.05030.07290.06090.109511.207514.7471-24.9279
65.37930.70250.54252.9761.25811.36250.0055-0.27930.35630.0631-0.00960.0349-0.022-0.01830.00410.0955-0.00940.05010.0233-0.0090.0847.983926.9324-20.2773
77.07871.37864.13692.48990.59393.80550.0298-0.31440.55890.18020.0312-0.1165-0.1370.1474-0.0610.2955-0.07240.07060.1316-0.0950.301818.186135.9753-13.0115
82.7822-0.64282.39423.4959-0.3264.62710.02310.1283-0.06480.0809-0.0439-0.01290.0371-0.13780.02080.05590.02420.04540.04340.02050.0956-13.431515.3514-53.7793
97.02881.6008-0.22573.5651-1.19831.0535-0.04560.40370.4884-0.06850.0829-0.0892-0.09070.0465-0.03730.13190.04930.0440.10710.07180.1423-9.955527.8474-60.1706
104.6824-1.462.13321.0189-1.05973.0805-0.067-0.34230.30690.05940.19260.1965-0.316-0.5731-0.12560.26350.02790.02180.12460.07770.3305-19.809832.8843-60.7908
114.79090.71785.22912.87853.119310.0579-0.23111.12180.2078-0.42110.0529-0.2854-0.39370.47860.17820.3385-0.03310.0830.50370.15770.514-9.856138.1166-70.4227
122.7960.8383-1.34983.4019-1.18692.9365-0.053-0.02160.1639-0.0449-0.01560.0008-0.0089-0.17610.06860.0563-0.0341-0.02770.06270.00770.0919-13.536112.9459-24.7821
135.9515-3.12130.13934.1554-2.07811.6552-0.1282-0.40980.1280.2590.31070.0091-0.1603-0.1492-0.18250.0912-0.02590.01220.09910.08180.213-14.76023.228-15.641
143.43421.0612-2.16522.5031-1.69213.706-0.25260.6036-0.7113-0.34440.0968-0.07040.4468-0.27860.15580.2003-0.00830.0490.158-0.04480.3728-6.5256-3.9658-24.3396
151.87930.9972-1.83771.5495-0.04683.5016-0.0293-0.2226-0.12980.0803-0.09860.0544-0.06280.04270.12790.2708-0.0217-0.01810.09610.02780.2096-22.3191-3.9248-5.2018
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 59
2X-RAY DIFFRACTION2A60 - 160
3X-RAY DIFFRACTION3A161 - 208
4X-RAY DIFFRACTION4A209 - 256
5X-RAY DIFFRACTION5B2 - 47
6X-RAY DIFFRACTION6B48 - 157
7X-RAY DIFFRACTION7B158 - 208
8X-RAY DIFFRACTION7B209 - 256
9X-RAY DIFFRACTION8C2 - 59
10X-RAY DIFFRACTION9C60 - 136
11X-RAY DIFFRACTION10C137 - 210
12X-RAY DIFFRACTION11C211 - 256
13X-RAY DIFFRACTION12D2 - 59
14X-RAY DIFFRACTION13D60 - 117
15X-RAY DIFFRACTION14D118 - 175
16X-RAY DIFFRACTION15D176 - 256

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