[English] 日本語
![](img/lk-miru.gif)
- PDB-3u0e: Crystal structure of beta-ketoacyl synthase from Brucella meliten... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3u0e | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of beta-ketoacyl synthase from Brucella melitensis in complex with fragment 9320 | ||||||
![]() | Beta-ketoacyl synthase | ||||||
![]() | TRANSFERASE / BETA-KETOACYL SYNTHASE / BRUCELLA MELITENSIS / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Fragments of Life / 8-methylquinolin-4-amine | ||||||
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 (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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 176.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 136.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 446.8 KB | Display | |
Data in XML | ![]() | 20.9 KB | Display | |
Data in CIF | ![]() | 33 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3lrfSC ![]() 3mqdC ![]() 3u0fC ![]() 4jv3C S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | |
Other databases |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 45643.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 2308 / Gene: fabB, BAB1_2173 / Plasmid: AVA0421 / Production host: ![]() ![]() References: UniProt: Q2YQQ9, beta-ketoacyl-[acyl-carrier-protein] synthase I | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-07K / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.4 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: MD PACT SCREEN, H12: 20% PEG 3350, 100MM BISTRISPROPANE PH 8.5, 200MM NA-MALONATE, CRYSTAL SOAKED 100MM MES PH 6.5, 250MM NACL, 30% PEG 3350, 10% GLYCEROL, BrabA.00113.a.A1.PW25441 AT 22. ...Details: MD PACT SCREEN, H12: 20% PEG 3350, 100MM BISTRISPROPANE PH 8.5, 200MM NA-MALONATE, CRYSTAL SOAKED 100MM MES PH 6.5, 250MM NACL, 30% PEG 3350, 10% GLYCEROL, BrabA.00113.a.A1.PW25441 AT 22.9MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 15, 2009 | |||||||||
Radiation | Monochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 1.6→50 Å / Num. all: 53371 / Num. obs: 53077 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 18.91 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 22.57 | |||||||||
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.55 / Num. unique all: 3843 / Rsym value: 0.22 / % possible all: 97.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: native structure 3lrf Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.131 / SU ML: 0.038 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 13.36 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.64 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 25.652 Å / Origin y: 1.872 Å / Origin z: 17.404 Å
|