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Open data
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Basic information
Entry | Database: PDB / ID: 6zz9 | ||||||
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Title | Crystal structure of CbpB from Streptococcus agalactiae | ||||||
![]() | CBS domain-containing protein | ||||||
![]() | SIGNALING PROTEIN / CBS / c-di-AMP | ||||||
Function / homology | CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / : / CBS domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mechaly, A.E. / Covaleda-Cortes, G. / Kaminski, P.A. | ||||||
![]() | ![]() Title: The c-di-AMP-binding protein CbpB modulates the level of ppGpp alarmone in Streptococcus agalactiae. Authors: Covaleda-Cortes, G. / Mechaly, A. / Brissac, T. / Baehre, H. / Devaux, L. / England, P. / Raynal, B. / Hoos, S. / Gominet, M. / Firon, A. / Trieu-Cuot, P. / Kaminski, P.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 | ![]() | 138.2 KB | Display | ![]() |
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PDB format | ![]() | 110.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 323.8 KB | Display | ![]() |
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Full document | ![]() | 326.5 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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: 19848.572 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: ykuL, C6N06_01440, D5F95_08070, DX05_08405, E8E04_03435, F5F86_02645, NCTC9828_00932, WA02_02795, WA05_04310 Production host: ![]() ![]() #2: Chemical | #3: Chemical | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.17 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion Details: 200 mM ammonium sulfate, 100 mM MES pH 6.5, 30% w/v PEG MME 5000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0716 Å / Relative weight: 1 |
Reflection | Resolution: 2.644→47.62 Å / Num. obs: 11037 / % possible obs: 98.94 % / Redundancy: 4.3 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.06712 / Rpim(I) all: 0.03644 / Rrim(I) all: 0.07653 / Net I/σ(I): 10.76 |
Reflection shell | Resolution: 2.644→2.739 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.346 / Num. unique obs: 1030 / CC1/2: 0.709 / CC star: 0.911 / Rpim(I) all: 0.7379 / Rrim(I) all: 1.538 / % possible all: 96.34 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 100.59 Å2
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Refine analyze | Luzzati coordinate error obs: 0.46 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.644→47.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.644→2.68 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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