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- PDB-6xnv: CRYSTAL STRUCTURE OF LISTERIA MONOCYTOGENES CBPB PROTEIN (LMO1009... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6xnv | ||||||
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Title | CRYSTAL STRUCTURE OF LISTERIA MONOCYTOGENES CBPB PROTEIN (LMO1009) IN COMPLEX WITH C-DI-AMP | ||||||
![]() | CBS domain-containing protein | ||||||
![]() | CYTOSOLIC PROTEIN / c-di-AMP binding protein | ||||||
Function / homology | CBS domain superfamily / CBS domain / CBS domain / Chem-2BA / CBS domain-containing protein / Lmo1009 protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Luo, S. / Tong, L. | ||||||
![]() | ![]() Title: (p)ppGpp and c-di-AMP Homeostasis Is Controlled by CbpB in Listeria monocytogenes. Authors: Peterson, B.N. / Young, M.K.M. / Luo, S. / Wang, J. / Whiteley, A.T. / Woodward, J.J. / Tong, L. / Wang, J.D. / Portnoy, D.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 | ![]() | 71.5 KB | Display | ![]() |
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PDB format | ![]() | 50.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 15.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6xnuC ![]() 3lqnS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18696.324 Da / Num. of mol.: 2 / Fragment: residues 12-150 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: 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: 2.2 Å3/Da / Density % sol: 44.07 % / Mosaicity: 0.245 ° |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 8 Details: 200 mM CaCl2, 100 mM imidazole, pH 8.0, 14% PEG 8,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 17, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→25 Å / Num. obs: 13591 / % possible obs: 98.2 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.039 / Rrim(I) all: 0.087 / Χ2: 1.053 / Net I/σ(I): 9 / Num. measured all: 64523 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3LQN Resolution: 2.4→24.93 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.6 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.85 Å2 / Biso mean: 64.4257 Å2 / Biso min: 31.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→24.93 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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