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- PDB-6etd: The Structure of the Mo-insertase domain Cnx1E from Arabidopsis t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6etd | ||||||
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Title | The Structure of the Mo-insertase domain Cnx1E from Arabidopsis thaliana in complex with AMP | ||||||
![]() | Molybdopterin biosynthesis protein CNX1 | ||||||
![]() | PLANT PROTEIN / 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 | ![]() | 330.8 KB | Display | ![]() |
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PDB format | ![]() | 269.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 774.7 KB | Display | ![]() |
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Full document | ![]() | 775.8 KB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 30.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6etfC ![]() 6ethC ![]() 6gaxC ![]() 6gb0C ![]() 6gb4C ![]() 6gb9C ![]() 6gbcC ![]() 6gbfC ![]() 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: 49779.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Oxidation of Cys-161 due to radiation damge / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q39054, molybdopterin molybdotransferase, molybdopterin adenylyltransferase |
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-Non-polymers , 5 types, 375 molecules ![](data/chem/img/AMP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-AMP / | ||||
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#3: Chemical | ChemComp-MG / | ||||
#4: Chemical | ChemComp-EDO / #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20 % (v/v) 1,2-Ehanediol; 10 % (w/v) PEG 8000; 0.3 M MgCl2; 0.3 M CaCl2; 0.1 M Tris/BICINE, 0.015 M MgxAMP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 3, 2017 / Details: Mirrors |
Radiation | Monochromator: SI111 double crystal with sagital bender / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.723→45.135 Å / Num. obs: 38415 / % possible obs: 66.8 % / Observed criterion σ(I): -3 / Redundancy: 4.43 % / Biso Wilson estimate: 29.06 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.073 / Rrim(I) all: 0.117 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.723→1.958 Å / Redundancy: 4.28 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2744 / CC1/2: 0.674 / Rpim(I) all: 0.555 / Rrim(I) all: 0.865 / % possible all: 15.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5G2R Resolution: 1.723→45.13 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.936 / SU R Cruickshank DPI: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.142 / SU Rfree Blow DPI: 0.129 / SU Rfree Cruickshank DPI: 0.125
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Displacement parameters | Biso mean: 31.37 Å2
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Refine analyze | Luzzati coordinate error obs: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.723→45.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.723→1.77 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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