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- PDB-8dq2: X-ray crystal structure of Hansschlegelia quercus lanmodulin (Lan... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dq2 | ||||||
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Title | X-ray crystal structure of Hansschlegelia quercus lanmodulin (LanM) with lanthanum (III) bound at pH 7 | ||||||
![]() | EF-hand domain-containing protein | ||||||
![]() | METAL BINDING PROTEIN / methanol dehydrogenase | ||||||
Function / homology | EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / calcium ion binding / CITRIC ACID / LANTHANUM (III) ION / EF-hand domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jung, J.J. / Lin, C.-Y. / Boal, A.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Enhanced rare-earth separation with a metal-sensitive lanmodulin dimer. Authors: Mattocks, J.A. / Jung, J.J. / Lin, C.Y. / Dong, Z. / Yennawar, N.H. / Featherston, E.R. / Kang-Yun, C.S. / Hamilton, T.A. / Park, D.M. / Boal, A.K. / Cotruvo Jr., J.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 | ![]() | 109.1 KB | Display | ![]() |
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PDB format | ![]() | 81.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 6.4 MB | Display | ![]() |
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Full document | ![]() | 6.4 MB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 28.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8fnrC ![]() 8fnsC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11923.299 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-LA / #3: Chemical | ChemComp-NA / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.77 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.01 M tri-sodium citrate, 27 % (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 29, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 41911 / % possible obs: 86.7 % / Redundancy: 6 % / Biso Wilson estimate: 17.53 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rpim(I) all: 0.052 / Rrim(I) all: 0.133 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.8→1.865 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.39 / Num. unique obs: 1053 / CC1/2: 0.612 / CC star: 0.868 / Rpim(I) all: 0.531 / Rrim(I) all: 1.13 / % possible all: 15.2 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 max: 81.42 Å2 / Biso mean: 26.0408 Å2 / Biso min: 8.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→40.11 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15
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