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- PDB-4r37: Crystal structure analysis of LpxA, a UDP-N-acetylglucosamine acy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4r37 | ||||||
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Title | Crystal structure analysis of LpxA, a UDP-N-acetylglucosamine acyltransferase from Bacteroides fragilis 9343 with UDP-GlcNAc | ||||||
![]() | Putative acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase | ||||||
![]() | TRANSFERASE / left-handed beta helix / UDP-N-acetylglucosamine acyltransferase | ||||||
Function / homology | ![]() acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase / acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase activity / lipid A biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fisher, A.J. / Chen, X. / Ngo, A. | ||||||
![]() | ![]() Title: Structures of Bacteroides fragilis uridine 5'-diphosphate-N-acetylglucosamine (UDP-GlcNAc) acyltransferase (BfLpxA). Authors: Ngo, A. / Fong, K.T. / Cox, D.L. / Chen, X. / Fisher, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130 KB | Display | ![]() |
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PDB format | ![]() | 97.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 25.9 KB | Display | |
Data in CIF | ![]() | 39.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4r36C ![]() 1lxaS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 1 - 255 / Label seq-ID: 21 - 275
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29906.020 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q5LH16, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase |
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-Non-polymers , 6 types, 526 molecules ![](data/chem/img/UD1.gif)
![](data/chem/img/PE5.gif)
![](data/chem/img/PG0.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PE5.gif)
![](data/chem/img/PG0.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-UD1 / | ||||
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#3: Chemical | ChemComp-PE5 / | ||||
#4: Chemical | ChemComp-PG0 / | ||||
#5: Chemical | #6: Chemical | ChemComp-CA / #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 28 % PEG600, 200 mM Calcium Acetate, 100 mM Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2014 / Details: Rh coated flat mirror |
Radiation | Monochromator: Si(111) Crystal. Side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12709 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→105.64 Å / Num. all: 45186 / Num. obs: 45186 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 30 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 5.6 / Num. unique all: 2959 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1LXA Resolution: 1.9→38 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.544 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.122 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 21.123 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→38 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 16020 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.9→1.952 Å / Total num. of bins used: 20
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