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Yorodumi- PDB-1o8q: The active site of the molybdenum cofactor biosenthetic protein d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1o8q | ||||||
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Title | The active site of the molybdenum cofactor biosenthetic protein domain Cnx1G | ||||||
Components | MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN | ||||||
Keywords | MOLYBDENUM COFACTOR BIOSYNTHESIS / CNX1G / MUTANTS | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Kuper, J. / Winking, J. / Hecht, H.J. / Schwarz, G. / Mendel, R.R. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2003 Title: The Active Site of the Molybdenum Cofactor Biosynthetic Protein Domain Cnx1G Authors: Kuper, J. / Winking, J. / 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 | 1o8q.cif.gz | 246.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o8q.ent.gz | 201.7 KB | Display | PDB format |
PDBx/mmJSON format | 1o8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/1o8q ftp://data.pdbj.org/pub/pdb/validation_reports/o8/1o8q | HTTPS FTP |
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-Related structure data
Related structure data | 1o8nC 1o8oC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 1 / Auth seq-ID: 5 - 162 / Label seq-ID: 5 - 162
NCS oper:
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-Components
#1: Protein | Mass: 17699.518 Da / Num. of mol.: 8 / Fragment: CNX1 G-DOMAIN, RESIDUES 462-628 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Strain: CV. COLUMBIA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): RK5206 / References: UniProt: Q39054 #2: Water | ChemComp-HOH / | Compound details | ENGINEERED MUTATION IN CHAIN A, SER 573 ALA ENGINEERED MUTATION IN CHAIN B, SER 573 ALA ENGINEERED ...ENGINEERED | Sequence details | DOMAIN DEFINITION | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.3 % |
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Crystal grow | pH: 7.7 / Details: 2.4 M SODIUM FORMIATE, pH 7.70 |
Crystal grow | *PLUS Method: unknown / Details: Schwarz, G., (2001) J. Mol. Biol., 312, 405. |
Components of the solutions | *PLUS Conc.: 2.4 M / Common name: sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Apr 15, 2002 / Details: OSMIX MIRROR OPTICS |
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→43.85 Å / Num. obs: 53034 / % possible obs: 97.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 4.3 / % possible all: 90.6 |
Reflection | *PLUS Highest resolution: 2.6 Å |
Reflection shell | *PLUS % possible obs: 90.6 % / Mean I/σ(I) obs: 3.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EAV Resolution: 2.6→43.85 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 8.369 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.499 / ESU R Free: 0.271 / 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: 42.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→43.85 Å
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Refine LS restraints |
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