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- PDB-3u0f: The structure of Beta-ketoacyl synthase from Brucella melitensis ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3u0f | ||||||
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Title | The structure of Beta-ketoacyl synthase from Brucella melitensis bound to the fragment 7-hydroxycoumarin | ||||||
![]() | Beta-ketoacyl synthase | ||||||
![]() | TRANSFERASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Beta-ketoacyl synthase | ||||||
Function / homology | ![]() beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
![]() | ![]() Title: Structural characterization of beta-ketoacyl ACP synthase I bound to platencin and fragment screening molecules at two substrate binding sites. Authors: Patterson, E.I. / Nanson, J.D. / Abendroth, J. / Bryan, C. / Sankaran, B. / Myler, P.J. / Forwood, J.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 189.2 KB | Display | ![]() |
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PDB format | ![]() | 147 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.5 KB | Display | ![]() |
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Full document | ![]() | 448 KB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 33.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3lrfSC ![]() 3mqdC ![]() 3u0eC ![]() 4jv3C 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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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 43652.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 2308 / Gene: BAB1_2173, fabB / Production host: ![]() ![]() References: UniProt: Q2YQQ9, beta-ketoacyl-[acyl-carrier-protein] synthase I |
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-Non-polymers , 5 types, 526 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/07L.gif)
![](data/chem/img/MOH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/07L.gif)
![](data/chem/img/MOH.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-07L / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.51 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: BrabA.00113.a at 22.94 mg/ml. 0.2M Sodium malonate, 0.1M Bis tris propane pH8.5, 20% PEG3350. BrabA.00113.a.A1 PW25441, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 9, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.25→39.275 Å / Num. obs: 109758 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.707 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 15.27 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: Direct phasing from previous structure Starting model: 3LRF Resolution: 1.25→39.275 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.974 / WRfactor Rfree: 0.1344 / WRfactor Rwork: 0.1216 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.947 / SU B: 0.859 / SU ML: 0.017 / SU R Cruickshank DPI: 0.0356 / SU Rfree: 0.0323 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 54.3 Å2 / Biso mean: 10.2718 Å2 / Biso min: 3.13 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→39.275 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.282 Å / Total num. of bins used: 20
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