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- PDB-7lm5: Crystal structure of the Zn(II)-bound AdcAII H65A mutant variant ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7lm5 | ||||||
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Title | Crystal structure of the Zn(II)-bound AdcAII H65A 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 | ![]() | 129.4 KB | Display | ![]() |
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PDB format | ![]() | 93.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.3 MB | Display | ![]() |
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Full document | ![]() | 4.3 MB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 15.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7lm6C ![]() 7lm7C ![]() 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: 32650.613 Da / Num. of mol.: 1 / Mutation: H65A 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 | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 40.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M imidazole pH 8.0, 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: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 15, 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: 2.4→36.16 Å / Num. obs: 10512 / % possible obs: 99.6 % / Redundancy: 7.5 % / Biso Wilson estimate: 38.25 Å2 / CC1/2: 0.998 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.298 / Num. unique obs: 1013 / CC1/2: 0.871 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3CX3 Resolution: 2.4→36.16 Å / SU ML: 0.2167 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.0247 / Stereochemistry target values: 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: 51.5 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→36.16 Å
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Refine LS restraints |
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LS refinement shell |
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