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- PDB-5xk7: Crystal structure of Isosesquilavandulyl Diphosphate Synthase fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xk7 | ||||||
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Title | Crystal structure of Isosesquilavandulyl Diphosphate Synthase from Streptomyces sp. strain CNH-189 in complex with DMAPP | ||||||
![]() | Undecaprenyl diphosphate synthase | ||||||
![]() | TRANSFERASE / prenyltransferase / antibiotic biosynthesis | ||||||
Function / homology | ![]() plastid membrane organization / dehydrodolichyl diphosphate synthase activity / Z-farnesyl diphosphate synthase activity / polyprenol biosynthetic process / polyprenyltransferase activity / response to cold / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ko, T.P. / Guo, R.T. / Liu, W. / Chen, C.C. / Gao, J. | ||||||
![]() | ![]() Title: "Head-to-Middle" and "Head-to-Tail" cis-Prenyl Transferases: Structure of Isosesquilavandulyl Diphosphate Synthase. Authors: Gao, J. / Ko, T.P. / Chen, L. / Malwal, S.R. / Zhang, J. / Hu, X. / Qu, F. / Liu, W. / Huang, J.W. / Cheng, Y.S. / Chen, C.C. / Yang, Y. / Zhang, Y. / Oldfield, E. / Guo, R.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 397.6 KB | Display | ![]() |
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PDB format | ![]() | 326.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 516.6 KB | Display | ![]() |
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Full document | ![]() | 526.9 KB | Display | |
Data in XML | ![]() | 44.6 KB | Display | |
Data in CIF | ![]() | 63.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xk3SC ![]() 5xk6C ![]() 5xk8C ![]() 5xk9C 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 26708.215 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: M4T4U9 |
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-Non-polymers , 6 types, 922 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/DMA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/DMA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-POP / #4: Chemical | ChemComp-MES / #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.23 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: PROTEIN: 10 mg/mL in 25 mM Tris-Cl (pH 7.5) and 150 mM NaCl RESERVOIR: 0.2 M (NH4)2SO4, 0.1 M MES pH 6.5, 30% PEG 5000MME SOAK: 5 mM MgCl2, 5 mM (NH4)4P2O7, 0.1 M MES pH 6.5, 30% PEG 5000MME, 10 mM DMAPP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 17, 2017 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→25 Å / Num. obs: 79758 / % possible obs: 98.5 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 1.91→1.98 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 7741 / CC1/2: 0.958 / % possible all: 97.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XK3 Resolution: 1.911→24.729 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.911→24.729 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 7.9075 Å / Origin y: 73.7212 Å / Origin z: 44.5425 Å
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Refinement TLS group | Selection details: all |