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- PDB-6btx: Structure of a bacterial metal transporter -

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Basic information

Entry
Database: PDB / ID: 6btx
TitleStructure of a bacterial metal transporter
ComponentsSolute carrier family 39 (Iron-regulated transporter)
KeywordsMETAL TRANSPORT / metal transporter
Function / homology
Function and homology information


iron ion transmembrane transporter activity / metal ion binding / plasma membrane
Similarity search - Function
Ferroportin-1 / Ferroportin1 (FPN1) / MFS transporter superfamily
Similarity search - Domain/homology
Chem-EDT / NICKEL (II) ION / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Ferreportin
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsJormakka, M. / Deshpande, C.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Nat Commun / Year: 2018
Title: Calcium is an essential cofactor for metal efflux by the ferroportin transporter family.
Authors: Deshpande, C.N. / Ruwe, T.A. / Shawki, A. / Xin, V. / Vieth, K.R. / Valore, E.V. / Qiao, B. / Ganz, T. / Nemeth, E. / Mackenzie, B. / Jormakka, M.
History
DepositionDec 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 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)49,3485
Polymers48,6011
Non-polymers7484
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-27 kcal/mol
Surface area17100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.072, 54.109, 72.442
Angle α, β, γ (deg.)90.000, 103.600, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Solute carrier family 39 (Iron-regulated 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6MLJ0

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Non-polymers , 5 types, 11 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-EDT / {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID


Mass: 292.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O8 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM Tris pH 8.0, 100 mM Na-acetate, 70 mM CaCl2, and 20% PEG500DME

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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: Aug 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→42.904 Å / Num. obs: 6989 / % possible obs: 96.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 57.16 Å2 / Net I/σ(I): 6.29
Reflection shellResolution: 3.2001→3.3145 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→42.904 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.24
RfactorNum. reflection% reflection
Rfree0.2552 697 9.98 %
Rwork0.2232 --
obs0.2264 6986 96.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.49 Å2 / Biso mean: 40.98 Å2 / Biso min: 30.32 Å2
Refinement stepCycle: final / Resolution: 3.2→42.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2810 0 45 7 2862
Biso mean--40.31 36.12 -
Num. residues----377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082920
X-RAY DIFFRACTIONf_angle_d0.5213975
X-RAY DIFFRACTIONf_chiral_restr0.034480
X-RAY DIFFRACTIONf_plane_restr0.005482
X-RAY DIFFRACTIONf_dihedral_angle_d6.5391674
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2001-3.44710.30531390.25741264140398
3.4471-3.79380.28341390.24491261140097
3.7938-4.34230.22871380.21281258139697
4.3423-5.46910.27531410.21541252139396
5.4691-42.90760.22311400.20941254139493

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