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Yorodumi- PDB-7lm6: Crystal structure of the Zn(II)-bound AdcAII H205L mutant variant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lm6 | ||||||
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Title | Crystal structure of the Zn(II)-bound AdcAII H205L mutant variant of Streptococcus pneumoniae | ||||||
Components | Adhesion protein | ||||||
Keywords | METAL BINDING PROTEIN / SBP / ATP-binding cassette transporter / Zn acquisition | ||||||
Function / homology | Adhesin B / metal ion transport / Adhesion lipoprotein / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / Prokaryotic membrane lipoprotein lipid attachment site profile. / cell adhesion / metal ion binding / Adhesion protein Function and homology information | ||||||
Biological species | Streptococcus pseudopneumoniae 5247 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.367 Å | ||||||
Authors | Luo, Z. / Zupan, M. / McDevitt, C.A. / Kobe, B. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Front Cell Infect Microbiol / Year: 2021 Title: Conformation of the Solute-Binding Protein AdcAII Influences Zinc Uptake in Streptococcus pneumoniae . Authors: Zupan, M.L. / Luo, Z. / Ganio, K. / Pederick, V.G. / Neville, S.L. / Deplazes, E. / Kobe, B. / McDevitt, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lm6.cif.gz | 109.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lm6.ent.gz | 83.9 KB | Display | PDB format |
PDBx/mmJSON format | 7lm6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lm6_validation.pdf.gz | 4 MB | Display | wwPDB validaton report |
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Full document | 7lm6_full_validation.pdf.gz | 4 MB | Display | |
Data in XML | 7lm6_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 7lm6_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/7lm6 ftp://data.pdbj.org/pub/pdb/validation_reports/lm/7lm6 | HTTPS FTP |
-Related structure data
Related structure data | 7lm5C 7lm7C 3cx3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 32692.695 Da / Num. of mol.: 1 / Mutation: H205L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pseudopneumoniae 5247 (bacteria) Gene: U753_04975 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: V8IJK5 | ||
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#2: Chemical | ChemComp-ZN / 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: 5.37 Å3/Da / Density % sol: 79.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M zinc acetate, 20% (w/v) polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 3.367→49.62 Å / Num. obs: 10715 / % possible obs: 99.5 % / Redundancy: 15.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.192 / Net I/σ(I): 15 |
Reflection shell | Resolution: 3.367→3.64 Å / Rmerge(I) obs: 0.581 / Num. unique obs: 2118 / CC1/2: 0.931 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CX3 Resolution: 3.367→49.619 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.367→49.619 Å
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Refine LS restraints |
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LS refinement shell |
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