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- PDB-3a1t: Crystal structue of the cytosolic domain of T. maritima FeoB iron... -

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Basic information

Entry
Database: PDB / ID: 3a1t
TitleCrystal structue of the cytosolic domain of T. maritima FeoB iron iransporter in GDP form II
ComponentsIron(II) transport protein B
KeywordsTRANSPORT PROTEIN / FeoB / iron transpoter / small GTPase / G protein / GDI
Function / homology
Function and homology information


ferrous iron transmembrane transporter activity / GTP binding / metal ion binding / plasma membrane
Similarity search - Function
Helix Hairpins - #1770 / 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. ...Helix Hairpins - #1770 / 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 / 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
GUANOSINE-5'-DIPHOSPHATE / Ferrous iron transport protein B
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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

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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)29,6742
Polymers29,2311
Non-polymers4431
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.152, 65.152, 104.798
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Iron(II) transport protein B


Mass: 29230.844 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-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growpH: 8.5 / Details: 25% PEG3350, 0.1M Tris-HCl, pH8.5, 0.1M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU
DetectorDate: Feb 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 31207

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Processing

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

3a1s


Resolution: 1.8→34.99 Å / SU ML: 0.54 / σ(F): 0.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2398 1199 5.02 %
Rwork0.1914 --
obs0.1939 23883 97.34 %
Solvent computationShrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.236 Å2 / ksol: 0.368 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→34.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 28 179 2234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072104
X-RAY DIFFRACTIONf_angle_d1.062879
X-RAY DIFFRACTIONf_dihedral_angle_d18.271786
X-RAY DIFFRACTIONf_chiral_restr0.068343
X-RAY DIFFRACTIONf_plane_restr0.004357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.87220.34481240.24912382X-RAY DIFFRACTION93
1.8722-1.95740.31231240.24012433X-RAY DIFFRACTION95
1.9574-2.06060.28841350.21632508X-RAY DIFFRACTION98
2.0606-2.18970.22891350.19762495X-RAY DIFFRACTION99
2.1897-2.35870.26131330.18552529X-RAY DIFFRACTION98
2.3587-2.5960.26861320.19542534X-RAY DIFFRACTION98
2.596-2.97150.25971370.19562586X-RAY DIFFRACTION99
2.9715-3.74310.20161380.17362609X-RAY DIFFRACTION100
3.7431-34.99630.21751410.17962608X-RAY DIFFRACTION95
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined1.8406-0.4539-0.32122.44140.07771.28550.03430.1742-0.03850.0866-0.23530.1756-0.0839-0.14150.140.34440.1033-0.07110.2861-0.06430.298226.47892.8043.2416
24.0641-0.2126-0.23520.5395-0.90551.84220.1921-0.60680.6981-0.10930.71920.16240.3701-0.4122-0.70790.43270.1063-0.09270.63040.02630.5728
3-0.0085-0.0829-0.06821.92460.47160.69930.10730.2759-0.4294-0.1351-0.25370.95430.2029-0.35110.19960.38810.0655-0.11290.4119-0.230.6718
40.90890.0212-0.31780.91410.8520.17950.16830.499-0.2005-0.3681-0.1844-0.21070.0702-0.0565-0.02150.39150.1461-0.0630.4165-0.07710.3305
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A 1-179
2X-RAY DIFFRACTION2chain A 180-189
3X-RAY DIFFRACTION3chain A 190-239
4X-RAY DIFFRACTION4chain A 240-268

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