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- PDB-7lm7: Crystal structure of the Zn(II)-bound AdcAII E280Q mutant variant... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7lm7 | ||||||
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Title | Crystal structure of the Zn(II)-bound AdcAII E280Q mutant variant of Streptococcus pneumoniae | ||||||
![]() | Adhesion protein | ||||||
![]() | 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![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Luo, Z. / Zupan, M. / McDevitt, C.A. / Kobe, B. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.9 KB | Display | ![]() |
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PDB format | ![]() | 93 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.4 MB | Display | ![]() |
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Full document | ![]() | 3.4 MB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 14.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7lm5C ![]() 7lm6C ![]() 3cx3S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 32716.699 Da / Num. of mol.: 1 / Mutation: E280Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: U753_04975 Production host: ![]() ![]() References: UniProt: V8IJK5 | ||||
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#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CL / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M imidazole pH 8.0, 0.2 M zinc acetate, 20% (w/v) polyethylene glycol (PEG) 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 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: 3.12→39.58 Å / Num. obs: 4870 / % possible obs: 98 % / Redundancy: 4 % / Biso Wilson estimate: 68.51 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.043 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 3.12→3.23 Å / Rmerge(I) obs: 0.19 / Num. unique obs: 412 / CC1/2: 0.87 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3CX3 Resolution: 3.12→39.58 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.37 / 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: 3.12→39.58 Å
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Refine LS restraints |
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LS refinement shell |
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