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- PDB-8c34: Aerobic light exposed 1.8 Angstrom crystal structure of cobalamin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8c34 | ||||||
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Title | Aerobic light exposed 1.8 Angstrom crystal structure of cobalamin binding domain belonging to a light-dependent transcription regulator TtCarH | ||||||
![]() | Probable transcriptional regulator | ||||||
![]() | TRANSCRIPTION / CarH / cobalamin / light-activated / transcription regulator | ||||||
Function / homology | ![]() cobalamin binding / DNA-binding transcription factor activity / DNA binding / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Poddar, H. / Leys, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Redox driven B 12 -ligand switch drives CarH photoresponse. Authors: Poddar, H. / Rios-Santacruz, R. / Heyes, D.J. / Shanmugam, M. / Brookfield, A. / Johannissen, L.O. / Levy, C.W. / Jeffreys, L.N. / Zhang, S. / Sakuma, M. / Colletier, J.P. / Hay, S. / ...Authors: Poddar, H. / Rios-Santacruz, R. / Heyes, D.J. / Shanmugam, M. / Brookfield, A. / Johannissen, L.O. / Levy, C.W. / Jeffreys, L.N. / Zhang, S. / Sakuma, M. / Colletier, J.P. / Hay, S. / Schiro, G. / Weik, M. / Scrutton, N.S. / Leys, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 187 KB | Display | ![]() |
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PDB format | ![]() | 147.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 42.8 KB | Display | |
Data in CIF | ![]() | 59.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8c31SC ![]() 8c32C ![]() 8c33C ![]() 8c35C ![]() 8c36C ![]() 8c37C ![]() 8c73C ![]() 8c76C S: Starting model for refinement 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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Unit cell |
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Components
#1: Protein | Mass: 23259.801 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-B12 / #3: Chemical | ChemComp-PEG / | #4: Chemical | ChemComp-PGE / | #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: 2.4 Å3/Da / Density % sol: 48.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Condition B3 from Morpheus screen (Molecular Dimensions) (0.09 M halogens, 0.1 M buffer system 1 pH 6.5, 30% v/v precipitant mix 3) Cryo-protected crystals exposed to bright 530 nm LED ...Details: Condition B3 from Morpheus screen (Molecular Dimensions) (0.09 M halogens, 0.1 M buffer system 1 pH 6.5, 30% v/v precipitant mix 3) Cryo-protected crystals exposed to bright 530 nm LED (Thorlabs) for 1-5 secs under aerobic conditions |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 14, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→52.1 Å / Num. obs: 81098 / % possible obs: 100 % / Redundancy: 25.7 % / CC1/2: 1 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.82→1.85 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3892 / CC1/2: 0.5 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8C31 Resolution: 1.82→52.1 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.82→52.1 Å
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LS refinement shell | Resolution: 1.82→1.87 Å /
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