+Open data
-Basic information
Entry | Database: PDB / ID: 1jw9 | ||||||
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Title | Structure of the Native MoeB-MoaD Protein Complex | ||||||
Components |
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Keywords | LIGASE / MoeB: modified Rossmann fold / (2) Cys-X-X-Cys Zinc-binding motifs / MoaD: ubiquitin-like fold | ||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.7 Å | ||||||
Authors | Lake, M.W. / Wuebbens, M.M. / Rajagopalan, K.V. / Schindelin, H. | ||||||
Citation | Journal: Nature / Year: 2001 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jw9.cif.gz | 78 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jw9.ent.gz | 58.5 KB | Display | PDB format |
PDBx/mmJSON format | 1jw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jw9_validation.pdf.gz | 453.3 KB | Display | wwPDB validaton report |
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Full document | 1jw9_full_validation.pdf.gz | 460 KB | Display | |
Data in XML | 1jw9_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 1jw9_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jw/1jw9 ftp://data.pdbj.org/pub/pdb/validation_reports/jw/1jw9 | HTTPS FTP |
-Related structure data
-Links
-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 |
-Components
#1: Protein | Mass: 26741.791 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MoeB / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P12282 | ||
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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.) Escherichia coli (E. coli) / Gene: MoaD / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P30748 | ||
#3: Chemical | ChemComp-ZN / | ||
#4: Chemical | #5: 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: 2.18 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: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å |
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 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: REFMAC Dictionary
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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 |