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- PDB-5nmu: Structure of hexameric CBS-CP12 protein from bloom-forming cyanob... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nmu | ||||||
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Title | Structure of hexameric CBS-CP12 protein from bloom-forming cyanobacteria | ||||||
![]() | CBS-CP12 | ||||||
![]() | PHOTOSYNTHESIS / Cystathionine beta synthase domain / fusion protein / redox-regulation of photosynthesis | ||||||
Function / homology | CP12 domain / CP12 domain / CP12 / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Similar to tr![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hackenberg, C. / Hakanpaa, J. / Antonyuk, S.V. / Dittmann, E. / Lamzin, V.S. | ||||||
![]() | ![]() Title: Structural and functional insights into the unique CBS-CP12 fusion protein family in cyanobacteria. Authors: Hackenberg, C. / Hakanpaa, J. / Cai, F. / Antonyuk, S. / Eigner, C. / Meissner, S. / Laitaoja, M. / Janis, J. / Kerfeld, C.A. / Dittmann, E. / Lamzin, V.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 216 KB | Display | ![]() |
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PDB format | ![]() | 174.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.9 KB | Display | ![]() |
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Full document | ![]() | 454.1 KB | Display | |
Data in XML | ![]() | 21.6 KB | Display | |
Data in CIF | ![]() | 30.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5nplSC ![]() 5nvdC 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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Unit cell |
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Components
#1: Protein | Mass: 23154.561 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Extra residues are left after TAG cleavage Source: (gene. exp.) ![]() Gene: IPF_2164 / Production host: ![]() ![]() #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 44 % / Description: hanging drop |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 8 Details: 300 mM Na Acetate, 25% PEG2000 MME, 100 mM HEPES buffer, pH 8.0, Vapor diffusion, Temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2015 / Details: KB mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→68.7 Å / Num. obs: 32084 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 39.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.038 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.15→2.22 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2725 / CC1/2: 0.811 / Rpim(I) all: 0.366 / % possible all: 96.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5NPL Resolution: 2.15→38.58 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 11.801 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.192 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.779 Å2
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Refinement step | Cycle: 1 / Resolution: 2.15→38.58 Å
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Refine LS restraints |
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