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Yorodumi- PDB-1uux: Structure of a molybdopterin-bound cnx1g domain links molybdenum ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uux | ||||||
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Title | Structure of a molybdopterin-bound cnx1g domain links molybdenum and copper metabolism | ||||||
Components | MOLYBDOPTERIN BIOSYNTHESIS CNX1 | ||||||
Keywords | CHELATASE / MOLYBDENUM COFACTOR BIOSYNTHESIS | ||||||
Function / homology | Function and homology information molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / nitrate reductase activity / auxin-activated signaling pathway / Mo-molybdopterin cofactor biosynthetic process / molybdenum ion binding / response to metal ion / ATP binding Similarity search - Function | ||||||
Biological species | ARABIDOPSIS THALIANA (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Kuper, J. / Llamas, A. / Hecht, H.J. / Mendel, R.R. / Schwarz, G. | ||||||
Citation | Journal: Nature / Year: 2004 Title: Structure of a Molybdopterin-Bound Cnx1G Domain Links Molybdenum and Copper Metabolism Authors: Kuper, J. / Llamas, A. / Hecht, H.J. / Mendel, R.R. / Schwarz, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uux.cif.gz | 51.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uux.ent.gz | 37.6 KB | Display | PDB format |
PDBx/mmJSON format | 1uux.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uux_validation.pdf.gz | 838.7 KB | Display | wwPDB validaton report |
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Full document | 1uux_full_validation.pdf.gz | 839.8 KB | Display | |
Data in XML | 1uux_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 1uux_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/1uux ftp://data.pdbj.org/pub/pdb/validation_reports/uu/1uux | HTTPS FTP |
-Related structure data
Related structure data | 1uuyC 1eavS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17198.902 Da / Num. of mol.: 1 / Fragment: G-DOMAIN, RESIDUES 462-624 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): RK5206 / References: UniProt: Q39054 |
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-Non-polymers , 6 types, 160 molecules
#2: Chemical | ChemComp-MTE / |
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#3: Chemical | ChemComp-PPI / |
#4: Chemical | ChemComp-IMD / |
#5: Chemical | ChemComp-FMT / |
#6: Chemical | ChemComp-CU1 / |
#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: 2.7 Å3/Da / Density % sol: 50.4 % |
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Crystal grow | pH: 7.8 / Details: 3.2 M SODIUM FORMATE ANAEROBIC, pH 7.80 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→22.88 Å / Num. obs: 28748 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.78 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 7.6484 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 7.78 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.91 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EAV Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.138 / SU ML: 0.041 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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