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Yorodumi- PDB-6gb9: The Structure of variant S328A of the Mo-insertase domain Cnx1E f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gb9 | ||||||
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Title | The Structure of variant S328A of the Mo-insertase domain Cnx1E from Arabidopsis thaliana in complex with AMP | ||||||
Components | Molybdopterin biosynthesis protein CNX1 | ||||||
Keywords | TRANSFERASE / 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: 1.67 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 | 6gb9.cif.gz | 330.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gb9.ent.gz | 268.9 KB | Display | PDB format |
PDBx/mmJSON format | 6gb9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gb/6gb9 ftp://data.pdbj.org/pub/pdb/validation_reports/gb/6gb9 | HTTPS FTP |
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-Related structure data
Related structure data | 6etdC 6etfC 6ethC 6gaxC 6gb0C 6gb4C 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: 48883.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Substitution of Arg-328 by alanine was engineered. / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CNX1, At5g20990, F22D1.6, T10F18.20 / Plasmid: pGplus-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 , 6 types, 434 molecules
#2: Chemical | ChemComp-AMP / | ||||||
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#3: Chemical | ChemComp-MG / | ||||||
#4: Chemical | #5: Chemical | ChemComp-CL / | #6: Chemical | #7: 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: 2.64 Å3/Da / Density meas: 53.52 Mg/m3 / Density % sol: 55.69 % / Description: isometric tetragonal prism |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M sodium formate, 0.1 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate, 0.1 M sodium potassium tartrate tetrahydrate, 0.1 M sodium oxamate; 0.1 M Tris BICINE pH 8.5; 10 % (w/v) ...Details: 0.1 M sodium formate, 0.1 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate, 0.1 M sodium potassium tartrate tetrahydrate, 0.1 M sodium oxamate; 0.1 M Tris BICINE pH 8.5; 10 % (w/v) PEG 4000, 20 % (v/v) glycerol |
-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 PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2017 / Details: Sagitally bended Si111 crystal |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→66.407 Å / Num. obs: 41927 / % possible obs: 66.1 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 25.16 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.097 / Rrim(I) all: 0.154 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.67→1.841 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.772 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2096 / CC1/2: 0.675 / Rpim(I) all: 0.615 / Rrim(I) all: 0.991 / % possible all: 13.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5G2R Resolution: 1.67→66.407 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.138 / SU Rfree Blow DPI: 0.126 / SU Rfree Cruickshank DPI: 0.121 Details: Data were corrected for anisotropy prior to refinement.
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Displacement parameters | Biso mean: 28.75 Å2
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Refine analyze | Luzzati coordinate error obs: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.67→66.407 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.66→1.7 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 27.288 Å / Origin y: 19.5638 Å / Origin z: 1.1865 Å
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Refinement TLS group | Selection details: { A|* } |