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- PDB-7z6n: Crystal structure of Zn2+-transporter BbZIP in a metal-stripped state -

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Basic information

Entry
Database: PDB / ID: 7z6n
TitleCrystal structure of Zn2+-transporter BbZIP in a metal-stripped state
ComponentsPutative membrane protein
KeywordsMEMBRANE PROTEIN / Zinc transporters / Zrt/Irt-like proteins (ZIPs) / solute carrier 39 (SLC39) family / BbZIP / transport mechanism / elevator mechanism
Function / homologyZinc/iron permease / ZIP Zinc transporter / zinc ion transmembrane transporter activity / plasma membrane / Zinc transporter ZIPB
Function and homology information
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsWiuf, A. / Steffen, J.H. / Becares, E.R. / Groenberg, C. / Mahato, D.R. / Rasmussen, S.G.F. / Andersson, M. / Croll, T. / Gotfryd, K. / Gourdon, P.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Council for Independent Research6108-00479 Denmark
CitationJournal: Sci Adv / Year: 2022
Title: The two-domain elevator-type mechanism of zinc-transporting ZIP proteins.
Authors: Wiuf, A. / Steffen, J.H. / Becares, E.R. / Gronberg, C. / Mahato, D.R. / Rasmussen, S.G.F. / Andersson, M. / Croll, T. / Gotfryd, K. / Gourdon, P.
History
DepositionMar 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative membrane protein
B: Putative membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9388
Polymers66,3612
Non-polymers5766
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-93 kcal/mol
Surface area23140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.493, 122.117, 101.733
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-401-

SO4

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Components

#1: Protein Putative membrane protein


Mass: 33180.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Strain: ATCC BAA-588 / NCTC 13252 / RB50 / Gene: BB2405 / Plasmid: pET15b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: A0A0H3LM39
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.79 Å3/Da / Density % sol: 55.94 %
Crystal growTemperature: 291 K / Method: lipidic cubic phase / pH: 4.5
Details: 100 mM NaOAc-HOAc pH = 4.5, 100-400 mM LiSO4 and 25-40 % PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Aug 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.57→41.17 Å / Num. obs: 22269 / % possible obs: 89.77 % / Redundancy: 15.5 % / CC1/2: 0.999 / CC star: 1 / Rpim(I) all: 0.1222 / Net I/av σ(I): 5.02 / Net I/σ(I): 5.02
Reflection shellResolution: 2.57→2.66 Å / Num. unique obs: 663 / CC1/2: 0.0526 / CC star: 0.316 / % possible all: 29.81

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIXdev_4234refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TSA

5tsa


Resolution: 2.57→41.17 Å / SU ML: 0.3624 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.6506
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rwork0.2876 13655 -
obs-14399 63.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.57→41.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3735 0 30 10 3775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00253831
X-RAY DIFFRACTIONf_angle_d0.72415228
X-RAY DIFFRACTIONf_chiral_restr0.0391662
X-RAY DIFFRACTIONf_plane_restr0.0069651
X-RAY DIFFRACTIONf_dihedral_angle_d11.68331275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.57-2.760.3945310.3143711X-RAY DIFFRACTION16.58
2.76-3.040.33611310.3181780X-RAY DIFFRACTION42.74
3.04-3.480.36121530.30562744X-RAY DIFFRACTION64.31
3.48-4.380.37331890.2894072X-RAY DIFFRACTION93.98
4.38-41.170.30772410.27794348X-RAY DIFFRACTION97.85

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