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

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Basic information

Entry
Database: PDB / ID: 5ayo
TitleCrystal structure of a bacterial homologue of iron transporter ferroportin in inward-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: 3.3 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 ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
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)49,1275
Polymers48,6011
Non-polymers5264
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-27 kcal/mol
Surface area18920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.530, 70.680, 101.790
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.35 Å3/Da / Density % sol: 47.68 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 4
Details: 100 mM Na-acetate, pH 4.0, 200-300 mM K-formate, 10 mM ZnSO4, 10-20 mM ZnCl2, 27-30% PEG550MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1.282 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 3.3→42.9 Å / Num. obs: 13103 / % possible obs: 98.5 % / Redundancy: 4 % / Net I/σ(I): 7.8
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: 3.3→42.857 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.9 / Stereochemistry target values: ML
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2846 1312 10.01 %
Rwork0.2352 11791 -
obs0.2403 13103 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.35 Å2 / Biso mean: 58.5393 Å2 / Biso min: 28.52 Å2
Refinement stepCycle: final / Resolution: 3.3→42.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2980 0 16 6 3002
Biso mean--60.84 46.13 -
Num. residues----406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023064
X-RAY DIFFRACTIONf_angle_d0.6424187
X-RAY DIFFRACTIONf_chiral_restr0.018515
X-RAY DIFFRACTIONf_plane_restr0.004511
X-RAY DIFFRACTIONf_dihedral_angle_d9.4821011
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3001-3.43220.34461440.30391308145299
3.4322-3.58830.29411450.26731311145699
3.5883-3.77740.36151440.25981354149899
3.7774-4.01390.27851490.2371297144699
4.0139-4.32350.31121460.22961335148199
4.3235-4.75810.23381440.21391301144599
4.7581-5.44550.30731450.23371299144498
5.4455-6.85620.32911430.25751300144398
6.8562-42.86040.22171520.19991286143897

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