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Yorodumi- PDB-1x07: Crystal structure of undecaprenyl pyrophosphate synthase in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x07 | ||||||
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Title | Crystal structure of undecaprenyl pyrophosphate synthase in complex with Mg and IPP | ||||||
Components | Undecaprenyl pyrophosphate synthetase | ||||||
Keywords | TRANSFERASE / enzyme-substrate complex | ||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Guo, R.-T. / Ko, T.-P. / Chen, A.P.-C. / Kuo, C.-J. / Wang, A.H.-J. / Liang, P.-H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1x07.cif.gz | 65.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x07.ent.gz | 47.6 KB | Display | PDB format |
PDBx/mmJSON format | 1x07.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1x07_validation.pdf.gz | 453 KB | Display | wwPDB validaton report |
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Full document | 1x07_full_validation.pdf.gz | 458.1 KB | Display | |
Data in XML | 1x07_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 1x07_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x0/1x07 ftp://data.pdbj.org/pub/pdb/validation_reports/x0/1x07 | HTTPS FTP |
-Related structure data
Related structure data | 1x06C 1x08C 1x09C 1v7uS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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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Details | The second part of the biological assembly is generated by the two fold axis: (x, -y, 39.71-z) |
-Components
#1: Protein | Mass: 28481.127 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET32 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 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 | ChemComp-IPE / |
#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: 2.06 Å3/Da / Density % sol: 40.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: MgCl2, IPP, Tris-HCL, NaCl, Triton X-100, PEG35000, ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002+ / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 4, 2004 / Details: mirrors |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 12260 / Num. obs: 12171 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 3.3 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: The monomer of A chain of PDB 1V7U Resolution: 2.2→50 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: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Rfactor Rfree error: 0.032
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