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- PDB-4ddo: 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: 4ddo | ||||||
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Title | Crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase ii from burkholderia vietnamiensis | ||||||
![]() | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | ||||||
![]() | TRANSFERASE / SSGCID / 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE II / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
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 | ![]() | 169.1 KB | Display | ![]() |
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PDB format | ![]() | 131.1 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 ![]() 4dfeC ![]() 4dheC ![]() 4dhkC ![]() 4dutC ![]() 4dz4C ![]() 4e4tC ![]() 4efiC ![]() 4eg0C ![]() 4egjC ![]() 4ek2C ![]() 4eqyC ![]() 4ewgC ![]() 4exqC ![]() 4f2gC ![]() 4f32C ![]() 4f3nC ![]() 4f3yC ![]() 4f4hC ![]() 4f7dC ![]() 4fk8C ![]() 4fryC ![]() 4g1kC ![]() 4g67C ![]() 4ghkC ![]() 4h3yC ![]() 4h3zC ![]() 4h4gC ![]() 1w0iS S: Starting model for refinement 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 FORMED FROM THE MONOMER IN THE ASYMMETRIC UNIT BY THE CRYSTALLOGRAPHIC OPERATIONS: -X, Y, -Z+0.5 |
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Components
#1: Protein | Mass: 46723.750 Da / Num. of mol.: 1 / Fragment: BuviA.00113.b.A1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A4JL30, beta-ketoacyl-[acyl-carrier-protein] synthase II |
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#2: Chemical | ChemComp-NA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.12 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8 Details: QIAGEN JCSG-2 B5: 1M LICL, 100MM TRIS PH 8, 20% PEG 6000, BUVIA.00113.B.A1 PS01317 AT 21.5MG/ML, 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: Jan 16, 2012 |
Radiation | Monochromator: RIGAKU VARIMAX / 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: 30274 / Num. obs: 29974 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 24.69 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 18.14 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2236 / Rsym value: 0.504 / % possible all: 88 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1w0i modified with CCP4 program CHAINSAW Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.234 / SU ML: 0.08 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
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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 mean: 16.1 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→1.95 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 3.161 Å / Origin y: 25.068 Å / Origin z: 17.995 Å
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