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Yorodumi- PDB-6gb4: The Structure of variant S328A of the Mo-insertase domain Cnx1E f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gb4 | ||||||
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Title | The Structure of variant S328A of the Mo-insertase domain Cnx1E from Arabidopsis thaliana in complex with AMP and molybdate | ||||||
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: 1.648 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 | 6gb4.cif.gz | 325.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gb4.ent.gz | 266.5 KB | Display | PDB format |
PDBx/mmJSON format | 6gb4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gb/6gb4 ftp://data.pdbj.org/pub/pdb/validation_reports/gb/6gb4 | HTTPS FTP |
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-Related structure data
Related structure data | 6etdC 6etfC 6ethC 6gaxC 6gb0C 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: 48883.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source 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 , 5 types, 260 molecules
#2: Chemical | ChemComp-AMP / | ||||
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#3: Chemical | ChemComp-MG / | ||||
#4: Chemical | #5: Chemical | ChemComp-MOO / | #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: 2.64 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 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 % glycerol; 0.015 M sodium molybdate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 22, 2018 / Details: mirrors |
Radiation | Monochromator: Bartels monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.648→90.136 Å / Num. obs: 53674 / % possible obs: 83 % / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Biso Wilson estimate: 30.95 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.023 / Rrim(I) all: 0.058 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 1.648→1.757 Å / Redundancy: 12.2 % / Rmerge(I) obs: 1.82 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2683 / CC1/2: 0.637 / Rpim(I) all: 0.538 / Rrim(I) all: 1.899 / % possible all: 24 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5G2R Resolution: 1.648→61.29 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.102 / SU Rfree Blow DPI: 0.098 / SU Rfree Cruickshank DPI: 0.096 Details: Data were corrected for anisotropy prior to refinement.
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Displacement parameters | Biso mean: 36.55 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.648→61.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.64→1.68 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 26.773 Å / Origin y: 19.5701 Å / Origin z: 0.8453 Å
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Refinement TLS group | Selection details: { A|* } |