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Open data
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Basic information
Entry | Database: PDB / ID: 1jw9 | ||||||
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Title | Structure of the Native MoeB-MoaD Protein Complex | ||||||
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![]() | LIGASE / MoeB: modified Rossmann fold / (2) Cys-X-X-Cys Zinc-binding motifs / MoaD: ubiquitin-like fold | ||||||
Function / homology | ![]() molybdopterin-synthase adenylyltransferase / molybdopterin-synthase adenylyltransferase activity / molybdopterin adenylyltransferase complex / molybdopterin synthase complex / ubiquitin-like modifier activating enzyme activity / sulfotransferase activity / thiosulfate sulfurtransferase activity / Mo-molybdopterin cofactor biosynthetic process / nucleotidyltransferase activity / nucleotide binding ... molybdopterin-synthase adenylyltransferase / molybdopterin-synthase adenylyltransferase activity / molybdopterin adenylyltransferase complex / molybdopterin synthase complex / ubiquitin-like modifier activating enzyme activity / sulfotransferase activity / thiosulfate sulfurtransferase activity / Mo-molybdopterin cofactor biosynthetic process / nucleotidyltransferase activity / nucleotide binding / protein homodimerization activity / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lake, M.W. / Wuebbens, M.M. / Rajagopalan, K.V. / Schindelin, H. | ||||||
![]() | ![]() Title: Mechanism of ubiquitin activation revealed by the structure of a bacterial MoeB-MoaD complex. Authors: Lake, M.W. / Wuebbens, M.M. / 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 | ![]() | 78 KB | Display | ![]() |
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PDB format | ![]() | 58.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.3 KB | Display | ![]() |
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Full document | ![]() | 460 KB | Display | |
Data in XML | ![]() | 17.2 KB | Display | |
Data in CIF | ![]() | 24.3 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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Details | The asymmetric unit contains a heterodimer comprised of (1) molecule of MoeB and (1) molecule of MoaD. The heterotetramer is generated by applying: -y+1,-x+1,1/2-z |
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Components
#1: Protein | Mass: 26741.791 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Protein | Mass: 8764.880 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#3: Chemical | ChemComp-ZN / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.51 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Lithium Sulfate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 27, 2000 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 37865 / Num. obs: 37865 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.71→1.78 Å / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 1.9 / % possible all: 99.3 |
Reflection | *PLUS % possible obs: 99.7 % |
Reflection shell | *PLUS % possible obs: 99.3 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 24.994 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / σ(F): 0 / % reflection Rfree: 4 % / Rfactor obs: 0.175 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |