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- PDB-1x06: Crystal structure of undecaprenyl pyrophosphate synthase in compl... -
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Basic information
Entry | Database: PDB / ID: 1x06 | ||||||
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Title | Crystal structure of undecaprenyl pyrophosphate synthase in complex with Mg, IPP and Fspp | ||||||
![]() | Undecaprenyl pyrophosphate synthetase | ||||||
![]() | TRANSFERASE / enzyme-substrate complex / metal coordination | ||||||
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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guo, R.-T. / Ko, T.-P. / Chen, A.P.-C. / Kuo, C.-J. / Wang, A.H.-J. / Liang, P.-H. | ||||||
![]() | ![]() Title: Crystal structures of undecaprenyl pyrophosphate synthase in complex with magnesium, isopentenyl pyrophosphate, and farnesyl thiopyrophosphate: roles of the metal ion and conserved residues in catalysis. Authors: Guo, R.T. / Ko, T.P. / Chen, A.P. / Kuo, C.J. / Wang, A.H. / Liang, P.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 | ![]() | 69.9 KB | Display | ![]() |
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PDB format | ![]() | 50.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1x07C ![]() 1x08C ![]() 1x09C ![]() 1v7uS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 28481.127 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P60472, ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] | ||
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#2: Chemical | ChemComp-PO4 / | ||
#3: Chemical | ChemComp-MG / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 41 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: MgCl2, IPP, FsPP, PEG35000, ethylene glycol, Triton X-100, NaCl, Tris-HCl, 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: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 12, 2004 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. all: 19231 / Num. obs: 19022 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.12 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.69 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1871 / % possible all: 95 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: chain A of PDB 1V7U Resolution: 1.9→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.018
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