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Yorodumi- PDB-7z6m: Crystal structure of Zn2+-transporter BbZIP in a cadmium bound state -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z6m | ||||||
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Title | Crystal structure of Zn2+-transporter BbZIP in a cadmium bound state | ||||||
Components | Putative membrane protein | ||||||
Keywords | MEMBRANE PROTEIN / Zinc transporters / Zrt/Irt-like proteins (ZIPs) / solute carrier 39 (SLC39) family / BbZIP / transport mechanism / elevator mechanism / METAL TRANSPORT | ||||||
Function / homology | Zinc/iron permease / ZIP Zinc transporter / zinc ion transmembrane transporter activity / plasma membrane / : / Zinc transporter ZIPB Function and homology information | ||||||
Biological species | Bordetella bronchiseptica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å | ||||||
Authors | Wiuf, 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
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z6m.cif.gz | 67.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z6m.ent.gz | 39.1 KB | Display | PDB format |
PDBx/mmJSON format | 7z6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z6m_validation.pdf.gz | 791.5 KB | Display | wwPDB validaton report |
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Full document | 7z6m_full_validation.pdf.gz | 793.8 KB | Display | |
Data in XML | 7z6m_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 7z6m_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/7z6m ftp://data.pdbj.org/pub/pdb/validation_reports/z6/7z6m | HTTPS FTP |
-Related structure data
Related structure data | 7z6nC 5tsaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33180.648 Da / Num. of mol.: 1 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 | ||
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#2: Chemical | ChemComp-CD / Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.81 % |
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Crystal grow | Temperature: 291 K / Method: lipidic cubic phase / pH: 7.4 Details: 100 mM HEPES-NaOH pH = 7.4, 100 mM CdCl2, 30% and PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Dec 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.51→45.51 Å / Num. obs: 10448 / % possible obs: 98.62 % / Redundancy: 7.6 % / Biso Wilson estimate: 79.76 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1628 / Rpim(I) all: 0.06329 / Rrim(I) all: 0.1751 / Net I/σ(I): 8.56 |
Reflection shell | Resolution: 2.51→2.6 Å / Redundancy: 7.1 % / Num. unique obs: 1011 / CC1/2: 0.41 / CC star: 0.762 / Rpim(I) all: 0.8814 / % possible all: 96.65 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TSA Resolution: 2.51→45.51 Å / SU ML: 0.4882 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 35.5047 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 90.69 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.51→45.51 Å
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Refine LS restraints |
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LS refinement shell |
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