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- PDB-4f32: Crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase II... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4f32 | ||||||
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Title | Crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase II from Burkholderia vietnamiensis in complex with platencin | ||||||
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![]() | Transferase/Antibiotic / SSGCID / 3-oxoacyl-[acyl-carrier-protein] synthase II / platencin / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / Transferase-Antibiotic complex | ||||||
Function / homology | ![]() beta-ketoacyl-[acyl-carrier-protein] synthase II / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
![]() | ![]() Title: Combining functional and structural genomics to sample the essential Burkholderia structome. Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 318.3 KB | Display | ![]() |
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PDB format | ![]() | 266.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3d63C ![]() 3dahC ![]() 3eizC ![]() 3ej2C ![]() 3ek2C ![]() 3ezoC ![]() 3f0fC ![]() 3ftpC ![]() 3gk0C ![]() 3gk3C ![]() 3gvfC ![]() 3gwaC ![]() 3gweC ![]() 3imlC ![]() 3sz8C ![]() 3t4cC ![]() 3tmlC ![]() 3tmqC ![]() 3txyC ![]() 3u7jC ![]() 3ue9C ![]() 3uk1C ![]() 3uk2C ![]() 3undC ![]() 3uptC ![]() 3urrC ![]() 3uw1C ![]() 3uw2C ![]() 3uw3C ![]() 3v2iC ![]() 3v7nC ![]() 3v8hC ![]() 3v9oC ![]() 3v9pC ![]() 3vavC ![]() 4ddoC ![]() 4dfeC ![]() 4dheC ![]() 4dhkC ![]() 4dutC ![]() 4dz4C ![]() 4e4tC ![]() 4efiC ![]() 4eg0C ![]() 4egjC ![]() 4ek2C ![]() 4eqyC ![]() 4ewgC ![]() 4exqC ![]() 4f2gC ![]() 4f3nC ![]() 4f3yC ![]() 4f4hC ![]() 4f7dC ![]() 4fk8C ![]() 4fryC ![]() 4g1kC ![]() 4g67C ![]() 4ghkC ![]() 4h3yC ![]() 4h3zC ![]() 4h4gC C: citing same article ( |
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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 | biological unit is a dimer, same as the asymmetric unit |
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Components
#1: Protein | Mass: 46803.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A4JL30, beta-ketoacyl-[acyl-carrier-protein] synthase II #2: Protein/peptide | | Mass: 273.330 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: from a strain of S. platensis, MA7339, recovered from a soil sample collected in Minut II (Mallorca) in Spain, Proc Natl Acad Sci U S A. 2007 May 1;104(18):7612-6 Source: (synth.) ![]() #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.61 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop Details: MD Morpheus a2: 10% PEG 8000, 20% Ethylene glycol, 30mM MgCl2, 30mM CaCl2, 100mM MES/Imidazole 6.5, BuviA.00113.b.A1 PS01317 at 20mg/ml with 1mM Platencin, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 3, 2012 / Details: RIGAKU VARIMAX HF | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: RIGAKU VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. all: 64282 / Num. obs: 63570 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 17.4 % / Biso Wilson estimate: 16.926 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 27.11 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 44.26 Å2 / Biso mean: 10.1563 Å2 / Biso min: 3.08 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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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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