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Yorodumi- PDB-6etd: The Structure of the Mo-insertase domain Cnx1E from Arabidopsis t... -
+Open data
-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 | ||||||
Components | Molybdopterin biosynthesis protein CNX1 | ||||||
Keywords | PLANT PROTEIN / Arabidopsis / Arabidopsis Proteins / Coenzymes / Metalloproteins / Catalytic Domain / Nucleotide Binding / Entropic Enzyme / Adenosine Monophosphate | ||||||
Function / homology | Function and homology information molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / nitrate reductase activity / auxin-activated signaling pathway / molybdenum ion binding / Mo-molybdopterin cofactor biosynthetic process / response to metal ion / ATP binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.723 Å | ||||||
Authors | Krausze, J. | ||||||
Citation | Journal: Biochem. J. / Year: 2018 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6etd.cif.gz | 330.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6etd.ent.gz | 269.6 KB | Display | PDB format |
PDBx/mmJSON format | 6etd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/6etd ftp://data.pdbj.org/pub/pdb/validation_reports/et/6etd | HTTPS FTP |
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-Related structure data
Related structure data | 6etfC 6ethC 6gaxC 6gb0C 6gb4C 6gb9C 6gbcC 6gbfC 5g2rS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-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.) Arabidopsis thaliana (thale cress) / Gene: CNX1, At5g20990, F22D1.6, T10F18.20 / Plasmid: pGpus-Cnx1E / Details (production host): pQE80 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): RK5204 References: UniProt: Q39054, molybdopterin molybdotransferase, molybdopterin adenylyltransferase |
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-Non-polymers , 5 types, 375 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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