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- PDB-4u82: Structure of S. aureus undecaprenyl diphosphate synthase in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4u82 | ||||||
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Title | Structure of S. aureus undecaprenyl diphosphate synthase in complex with FSPP and sulfate | ||||||
![]() | Isoprenyl transferase | ||||||
![]() | TRANSFERASE / Alkyl and Aryl Transferases / Anti-Bacterial Agents / Benzoates / Biosynthetic Pathways / Cell Wall / Diphosphonates / Drug Discovery / High-Throughput Screening Assays / Methicillin / Microbial Sensitivity Tests / Pyrrolidinones / Staphylococcus aureus / Terpenes | ||||||
Function / homology | ![]() Transferases; Transferring alkyl or aryl groups, other than methyl groups / prenyltransferase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhu, W. / Oldfield, E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Antibacterial drug leads: DNA and enzyme multitargeting. Authors: Zhu, W. / Wang, Y. / Li, K. / Gao, J. / Huang, C.H. / Chen, C.C. / Ko, T.P. / Zhang, Y. / Guo, R.T. / Oldfield, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.2 KB | Display | ![]() |
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PDB format | ![]() | 46.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 644.8 KB | Display | ![]() |
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Full document | ![]() | 645.7 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 16.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wyiC ![]() 3wyjC ![]() 4u8aC ![]() 4u8bC ![]() 4u8cC ![]() 4h8eS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29902.199 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P60477, Transferases; Transferring alkyl or aryl groups, other than methyl groups |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-FPS / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.06 % |
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Crystal grow | Temperature: 298 K / Method: evaporation Details: 100 mM MES sodium, pH 6.5, 200 mM ammonium sulfate, 25% PEG5000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 24, 2012 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→50 Å / Num. obs: 32040 / % possible obs: 99.5 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 34.5714 |
Reflection shell | Resolution: 1.66→1.69 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 4.5714 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4H8E Resolution: 1.66→46.33 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.627 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.02 Å2 / Biso mean: 20.106 Å2 / Biso min: 10.08 Å2
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Refinement step | Cycle: final / Resolution: 1.66→46.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.66→1.703 Å / Total num. of bins used: 20
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