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- PDB-8c31: Dark state 1.8 Angstrom crystal structure of cobalamin binding do... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8c31 | ||||||
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Title | Dark state 1.8 Angstrom crystal structure of cobalamin binding domain belonging to a light-dependent transcription regulator TtCarH obtained under aerobic condition | ||||||
![]() | 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 | ![]() | 343.5 KB | Display | ![]() |
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PDB format | ![]() | 277.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 40.5 KB | Display | |
Data in CIF | ![]() | 55.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8c32C ![]() 8c33C ![]() 8c34C ![]() 8c35C ![]() 8c36C ![]() 8c37C ![]() 8c73C ![]() 8c76C ![]() 5c8aS 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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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 23259.801 Da / Num. of mol.: 4 / Mutation: No Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 7 types, 509 molecules ![](data/chem/img/BR.gif)
![](data/chem/img/B12.gif)
![](data/chem/img/5AD.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/B12.gif)
![](data/chem/img/5AD.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-B12 / #4: Chemical | ChemComp-5AD / #5: Chemical | #6: Chemical | ChemComp-PGE / | #7: Chemical | ChemComp-EDO / #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.92 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Condition B3 from Morpheus screen (Molecular Diensions) (0.09 M halogens, 0.1 M buffer system 1 pH 6.5, 30% v/v precipitant mix 3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 9, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→61.18 Å / Num. obs: 84476 / % possible obs: 96.7 % / Redundancy: 13.6 % / CC1/2: 1 / Rrim(I) all: 0.086 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.8→1.83 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 4123 / CC1/2: 0.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5C8A Resolution: 1.8→61.18 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 6.565 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.085 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→61.18 Å
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Refine LS restraints |
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