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Open data
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Basic information
Entry | Database: PDB / ID: 6zza | ||||||
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Title | Crystal structure of CbpB in complex with c-di-AMP | ||||||
![]() | CBS domain-containing protein | ||||||
![]() | SIGNALING PROTEIN / CBS / c-di-AMP | ||||||
Function / homology | CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Chem-2BA / CBS domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mechaly, A.E. / Covaleda-Cortes, G. / Kaminski, P.A. | ||||||
![]() | ![]() Title: Crystal structure of CbpB in complex with c-di-AMP Authors: Mechaly, A.E. / Covaleda-Cortes, G. / 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 | ![]() | 82.2 KB | Display | ![]() |
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PDB format | ![]() | 57.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6zz9S 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19848.572 Da / Num. of mol.: 1 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: ![]() ![]() |
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#2: Chemical | ChemComp-2BA / ( |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.82 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / Details: 200 mM ammonium sulfate, 20% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2.491→31.05 Å / Num. obs: 6110 / % possible obs: 99.12 % / Redundancy: 5.3 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1012 / Rpim(I) all: 0.04755 / Rrim(I) all: 0.1124 / Net I/σ(I): 9.79 |
Reflection shell | Resolution: 2.491→2.58 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.6201 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 578 / CC1/2: 0.798 / CC star: 0.942 / Rpim(I) all: 0.2914 / Rrim(I) all: 0.6887 / % possible all: 93.21 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6ZZ9 Resolution: 2.491→31.05 Å / Cross valid method: THROUGHOUT Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 67.54 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.491→31.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.491→2.78 Å
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