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Open data
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Basic information
Entry | Database: PDB / ID: 3bii | ||||||
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Title | Crystal Structure of Activated MPT Synthase | ||||||
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![]() | TRANSFERASE / MPT synthase / Moco biosynthesis / MoaE / MoaD / ubiquitin-like / beta-hammerhead fold / Molybdenum cofactor biosynthesis | ||||||
Function / homology | ![]() molybdopterin adenylyltransferase complex / molybdopterin synthase complex / molybdopterin synthase / molybdopterin synthase activity / Mo-molybdopterin cofactor biosynthetic process / nucleotide binding / protein homodimerization activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Daniels, J.N. / Schindelin, H. | ||||||
![]() | ![]() Title: Crystal structure of a molybdopterin synthase-precursor Z complex: insight into its sulfur transfer mechanism and its role in molybdenum cofactor deficiency. Authors: Daniels, J.N. / Wuebbens, M.M. / Rajagopalan, K.V. / Schindelin, H. #1: ![]() Title: Structural studies of molybdopterin synthase provide insights into its catalytic mechanism Authors: Rudolph, M.J. / Wuebbens, M.M. / Turque, O. / Rajagopalan, K.V. / Schindelin, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.5 KB | Display | ![]() |
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PDB format | ![]() | 44.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436 KB | Display | ![]() |
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Full document | ![]() | 437.8 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 15.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 8780.944 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Protein | Mass: 16871.826 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.98 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.1 Ammonium sulfate and .1M HEPES pH=7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Date: Jan 1, 2002 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 9359 / % possible obs: 87.6 % / Rmerge(I) obs: 0.096 / Χ2: 1.505 / Net I/σ(I): 13 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Resolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.891 / SU B: 20.561 / SU ML: 0.243 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.339 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.916 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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