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- PDB-4qyr: Streptomyces platensis isomigrastatin ketosynthase domain MgsE KS3 -
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Open data
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Basic information
Entry | Database: PDB / ID: 4qyr | ||||||
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Title | Streptomyces platensis isomigrastatin ketosynthase domain MgsE KS3 | ||||||
![]() | AT-less polyketide synthase | ||||||
![]() | TRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro / alpha-beta structure | ||||||
Function / homology | ![]() phosphopantetheine binding / antibiotic biosynthetic process / transferase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, Y. / Li, H. / Endres, M. / Babnigg, J. / Bingman, C.A. / Yennamalli, R. / Lohman, J.R. / Ma, M. / Shen, B. / Phillips Jr., G.N. ...Kim, Y. / Li, H. / Endres, M. / Babnigg, J. / Bingman, C.A. / Yennamalli, R. / Lohman, J.R. / Ma, M. / Shen, B. / Phillips Jr., G.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro) | ||||||
![]() | ![]() Title: Structural and evolutionary relationships of "AT-less" type I polyketide synthase ketosynthases. Authors: Lohman, J.R. / Ma, M. / Osipiuk, J. / Nocek, B. / Kim, Y. / Chang, C. / Cuff, M. / Mack, J. / Bigelow, L. / Li, H. / Endres, M. / Babnigg, G. / Joachimiak, A. / Phillips, G.N. / Shen, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 243.6 KB | Display | ![]() |
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PDB format | ![]() | 195.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4opeC ![]() 4opfC ![]() 4oqjC ![]() 4tktC ![]() 4wkyC ![]() 4zdnC ![]() 4na1S C: citing same article ( S: Starting model for refinement |
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Similar structure data | |
Other databases |
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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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Details | a dimer is generated by applying x,y,z and y,x,-z to the asymmetric unit. |
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Components
#1: Protein | Mass: 65851.141 Da / Num. of mol.: 1 / Fragment: UNP residues 2542-3153 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pMCSG73 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-ACY / |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.81 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M sodium acetate, 0.1 M HEPES pH 7.5, 22%(w/v) PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 17, 2014 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 18196 / Num. obs: 18196 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 53.25 Å2 / Rsym value: 0.103 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 888 / Rsym value: 0.754 / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4NA1 Resolution: 2.902→36.354 Å / SU ML: 0.31 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.59 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.902→36.354 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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