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- PDB-3a1w: Crystal structue of the G domain of T. maritima FeoB iron iransporter -

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Basic information

Entry
Database: PDB / ID: 3a1w
TitleCrystal structue of the G domain of T. maritima FeoB iron iransporter
ComponentsIron(II) transport protein B
KeywordsTRANSPORT PROTEIN / FeoB / iron transporter / small GTPase / GDI / G protein
Function / homology
Function and homology information


ferrous iron transmembrane transporter activity / GTP binding / metal ion binding / plasma membrane
Similarity search - Function
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. / Nucleoside transporter/FeoB GTPase, Gate 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. / Nucleoside transporter/FeoB GTPase, Gate domain / Nucleoside recognition / GTP binding domain / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ferrous iron transport protein B
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9001 Å
AuthorsHattori, M. / Ishitani, R. / Nureki, O.
CitationJournal: Structure / Year: 2009
Title: Structural basis of novel interactions between the small-GTPase and GDI-like domains in prokaryotic FeoB iron transporter
Authors: Hattori, M. / Jin, Y. / Nishimasu, H. / Tanaka, Y. / Mochizuki, M. / Uchiumi, T. / Ishitani, R. / Ito, K. / Nureki, O.
History
DepositionApr 22, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 28, 2025Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Iron(II) transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6312
Polymers18,5341
Non-polymers961
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.175, 63.175, 116.882
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Iron(II) transport protein B


Mass: 18534.455 Da / Num. of mol.: 1 / Fragment: UNP residues 17-269
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0051 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q9WXQ8
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.15 Å3/Da / Density % sol: 60.9 %
Crystal growDetails: 1.1-1.3M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A
DetectorDate: Jan 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 21851

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Processing

SoftwareName: PHENIX / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A1S

3a1s


Resolution: 1.9001→41.746 Å / SU ML: 0.69 / σ(F): 0.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.219 952 5 %
Rwork0.1867 --
obs0.1882 19031 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 77.784 Å2 / ksol: 0.389 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9001→41.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1242 0 5 104 1351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071269
X-RAY DIFFRACTIONf_angle_d1.0361730
X-RAY DIFFRACTIONf_dihedral_angle_d17.501451
X-RAY DIFFRACTIONf_chiral_restr0.068208
X-RAY DIFFRACTIONf_plane_restr0.003218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8998-20.31141270.28082429X-RAY DIFFRACTION95
2-2.12530.24881330.2242510X-RAY DIFFRACTION97
2.1253-2.28930.24561340.19722542X-RAY DIFFRACTION98
2.2893-2.51970.22021340.18042565X-RAY DIFFRACTION99
2.5197-2.88420.21521380.18262611X-RAY DIFFRACTION99
2.8842-3.63350.19921390.16642634X-RAY DIFFRACTION100
3.6335-41.75590.21121470.1822788X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 2.1148 Å / Origin y: -21.5756 Å / Origin z: -17.9074 Å
111213212223313233
T0.1317 Å2-0.0043 Å20.0353 Å2-0.3077 Å2-0.0168 Å2--0.2238 Å2
L3.0398 °2-0.4972 °2-1.8213 °2-1.352 °20.3652 °2--3.699 °2
S-0.2394 Å °-0.0749 Å °-0.1812 Å °0.0141 Å °-0.0516 Å °0.1051 Å °0.2113 Å °-0.2075 Å °0.2427 Å °
Refinement TLS groupSelection details: chain A 15-177

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