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- PDB-6gbf: The Structure of variant R369A of the Mo-insertase domain Cnx1E f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gbf | ||||||
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Title | The Structure of variant R369A of the Mo-insertase domain Cnx1E from Arabidopsis thaliana in complex with AMP | ||||||
![]() | Molybdopterin biosynthesis protein CNX1 | ||||||
![]() | TRANSFERASE / Arabidopsis / Arabidopsis Proteins / Coenzymes / Metalloproteins / Catalytic Domain / Nucleotide Binding / Entropic Enzyme / Adenosine Monophosphate | ||||||
Function / homology | ![]() glycine receptor clustering / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / establishment of synaptic specificity at neuromuscular junction / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / gamma-aminobutyric acid receptor clustering / nitrate reductase activity / auxin-activated signaling pathway / Mo-molybdopterin cofactor biosynthetic process ...glycine receptor clustering / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / establishment of synaptic specificity at neuromuscular junction / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / gamma-aminobutyric acid receptor clustering / nitrate reductase activity / auxin-activated signaling pathway / Mo-molybdopterin cofactor biosynthetic process / molybdenum ion binding / postsynaptic neurotransmitter receptor diffusion trapping / response to metal ion / dendrite / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Krausze, J. | ||||||
![]() | ![]() Title: The functional principle of eukaryotic molybdenum insertases. Authors: Krausze, J. / Hercher, T.W. / Zwerschke, D. / Kirk, M.L. / Blankenfeldt, W. / Mendel, R.R. / Kruse, T. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 328.7 KB | Display | ![]() |
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PDB format | ![]() | 268.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 776.6 KB | Display | ![]() |
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Full document | ![]() | 776.7 KB | Display | |
Data in XML | ![]() | 20 KB | Display | |
Data in CIF | ![]() | 31.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6etdC ![]() 6etfC ![]() 6ethC ![]() 6gaxC ![]() 6gb0C ![]() 6gb4C ![]() 6gb9C ![]() 6gbcC ![]() 5g2rS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48813.090 Da / Num. of mol.: 1 / Mutation: R369A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q39054, molybdopterin molybdotransferase, molybdopterin adenylyltransferase |
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-Non-polymers , 5 types, 403 molecules ![](data/chem/img/AMP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-AMP / | ||||
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#3: Chemical | ChemComp-MG / | ||||
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.52 % / Description: isometric tetragonal prism |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M imidazole, 0.1 M MES pH 6.5; 0.06 M sodium nitrate, 0.06 M sodium phosphate, 0.06 M ammonium sulfate; 20 % (v/v) PEG 500 MME, 10 % PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2017 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.712→66.34 Å / Num. obs: 42230 / % possible obs: 71.7 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 28.63 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.034 / Rrim(I) all: 0.054 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.712→1.849 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2113 / CC1/2: 0.615 / Rpim(I) all: 0.665 / Rrim(I) all: 1.022 / % possible all: 17.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5G2R Resolution: 1.712→25.07 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU R Cruickshank DPI: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.126 / SU Rfree Blow DPI: 0.115 / SU Rfree Cruickshank DPI: 0.111 Details: The data were corrected for anisotropy prior to refinement.
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Displacement parameters | Biso mean: 33.22 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.712→25.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.71→1.76 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 27.1825 Å / Origin y: 19.543 Å / Origin z: 1.1463 Å
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Refinement TLS group | Selection details: { A|* } |