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- PDB-5ayn: Crystal structure of a bacterial homologue of iron transporter fe... -

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Basic information

Entry
Database: PDB / ID: 5ayn
TitleCrystal structure of a bacterial homologue of iron transporter ferroportin in outward-facing state
ComponentsSolute carrier family 39 (Iron-regulated transporter)
KeywordsTRANSPORT PROTEIN / alpha helical
Function / homologyFerroportin-1 / Ferroportin1 (FPN1) / iron ion transmembrane transporter activity / MFS transporter superfamily / metal ion binding / plasma membrane / : / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Ferreportin
Function and homology information
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.202 Å
AuthorsTaniguchi, R. / Kato, H.E. / Font, J. / Deshpande, C.N. / Ishitani, R. / Jormakka, M. / Nureki, O.
CitationJournal: Nat Commun / Year: 2015
Title: Outward- and inward-facing structures of a putative bacterial transition-metal transporter with homology to ferroportin
Authors: Taniguchi, R. / Kato, H.E. / Font, J. / Deshpande, C.N. / Wada, M. / Ito, K. / Ishitani, R. / Jormakka, M. / Nureki, O.
History
DepositionAug 25, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 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

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Assembly

Deposited unit
A: Solute carrier family 39 (Iron-regulated transporter)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,84911
Polymers48,6011
Non-polymers3,24810
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint0 kcal/mol
Surface area18280 Å2
Unit cell
Length a, b, c (Å)56.638, 84.629, 96.809
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Solute carrier family 39 (Iron-regulated transporter) / membrane transporter


Mass: 48600.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus (bacteria) / Strain: ATCC 15356 / DSM 50701 / NCIB 9529 / HD100 / Gene: slc39, Bd2019 / Plasmid: pET variant / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: Q6MLJ0
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8.5
Details: 100 mM Tris, pH 8.5, 100 mM NaK-tartrate, 100 mM KNO3, 30% PEG550MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→48.404 Å / Num. obs: 24182 / % possible obs: 99.9 % / Redundancy: 7.3 % / Net I/σ(I): 10.6
Reflection shell
Diffraction-IDRejects
10
10
10
10
10
10
10
10
10
10
10
10
10
10
10
10
10
10
10

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementResolution: 2.202→48.404 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2398 1208 5 %
Rwork0.1968 22974 -
obs0.199 24182 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.55 Å2 / Biso mean: 33.3048 Å2 / Biso min: 15.33 Å2
Refinement stepCycle: final / Resolution: 2.202→48.404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3069 0 157 58 3284
Biso mean--50.85 33.2 -
Num. residues----405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073315
X-RAY DIFFRACTIONf_angle_d1.0334471
X-RAY DIFFRACTIONf_chiral_restr0.038524
X-RAY DIFFRACTIONf_plane_restr0.005535
X-RAY DIFFRACTIONf_dihedral_angle_d14.2191166
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2021-2.29030.27971310.221725032634
2.2903-2.39450.27231320.21124882620
2.3945-2.52080.25531310.199525192650
2.5208-2.67870.23691350.192125452680
2.6787-2.88550.25541320.187625132645
2.8855-3.17580.22331340.191925452679
3.1758-3.63530.24261350.194825592694
3.6353-4.57950.24371350.194725852720
4.5795-48.41620.21881430.197927172860

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