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- PDB-4h2m: Structure of E. coli undecaprenyl diphosphate synthase in complex... -
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Basic information
Entry | Database: PDB / ID: 4h2m | ||||||
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Title | Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-1408 | ||||||
![]() | Undecaprenyl pyrophosphate synthase | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / prenyl transferase inhibitor complex / alpha-helix / prenyl transferase / cell wall biosynthesis / farnesyl diphosphate binding / isopentenyl diphosphate binding / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() Gram-negative-bacterium-type cell wall biogenesis / ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] / di-trans,poly-cis-undecaprenyl-diphosphate synthase activity / polyprenol biosynthetic process / small molecule binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / magnesium ion binding ...Gram-negative-bacterium-type cell wall biogenesis / ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] / di-trans,poly-cis-undecaprenyl-diphosphate synthase activity / polyprenol biosynthetic process / small molecule binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / magnesium ion binding / protein homodimerization activity / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhu, W. / Oldfield, E. | ||||||
![]() | ![]() Title: Antibacterial drug leads targeting isoprenoid biosynthesis. Authors: Zhu, W. / Zhang, Y. / Sinko, W. / Hensler, M.E. / Olson, J. / Molohon, K.J. / Lindert, S. / Cao, R. / Li, K. / Wang, K. / Wang, Y. / Liu, Y.L. / Sankovsky, A. / de Oliveira, C.A. / Mitchell, ...Authors: Zhu, W. / Zhang, Y. / Sinko, W. / Hensler, M.E. / Olson, J. / Molohon, K.J. / Lindert, S. / Cao, R. / Li, K. / Wang, K. / Wang, Y. / Liu, Y.L. / Sankovsky, A. / de Oliveira, C.A. / Mitchell, D.A. / Nizet, V. / McCammon, J.A. / 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 | ![]() | 98.8 KB | Display | ![]() |
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PDB format | ![]() | 76 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3sgtC ![]() 3sgvC ![]() 3sgxC ![]() 3sh0C ![]() 4h2jC ![]() 4h2oC ![]() 4h38C ![]() 4h3aC ![]() 4h3cC ![]() 4h8eC ![]() 2e98S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28481.127 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P60472, ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.19 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 5% PEG4000, pH 7.5, 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: Feb 4, 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: 1.78→50 Å / Num. obs: 47258 / % possible obs: 99.9 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 29.1 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.6 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2E98 Resolution: 1.78→43.46 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.489 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.123 / 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: 123.11 Å2 / Biso mean: 29.7577 Å2 / Biso min: 11.82 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→43.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.827 Å / Total num. of bins used: 20
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