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Yorodumi- PDB-4r36: Crystal structure analysis of LpxA, a UDP-N-acetylglucosamine acy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r36 | ||||||
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Title | Crystal structure analysis of LpxA, a UDP-N-acetylglucosamine acyltransferase from Bacteroides fragilis 9343 | ||||||
Components | Putative acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase | ||||||
Keywords | TRANSFERASE / left-handed beta helix / UDP-N-acetylglucosamine acyltransferase | ||||||
Function / homology | Function and homology information 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 | Bacteroides fragilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Ngo, A. / Fong, K. / Cox, D. / Fisher, A. / Chen, X. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r36.cif.gz | 124.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r36.ent.gz | 94.7 KB | Display | PDB format |
PDBx/mmJSON format | 4r36.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4r36_validation.pdf.gz | 766.7 KB | Display | wwPDB validaton report |
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Full document | 4r36_full_validation.pdf.gz | 769.8 KB | Display | |
Data in XML | 4r36_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 4r36_validation.cif.gz | 37.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/4r36 ftp://data.pdbj.org/pub/pdb/validation_reports/r3/4r36 | HTTPS FTP |
-Related structure data
Related structure data | 4r37C 1lxaS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Bacteroides fragilis (bacteria) / Strain: ATCC 25285 / NCTC 9343 / Gene: lpxA, BF9343_0789 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) References: UniProt: Q5LH16, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase |
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-Non-polymers , 5 types, 461 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PE5 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.68 % |
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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: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å |
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→105.39 Å / Num. all: 45045 / Num. obs: 45045 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 35.3 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 4.9 / Num. unique all: 2836 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1LXA Resolution: 1.9→38 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.607 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.126 / ESU R Free: 0.12 / 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: 26.097 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: 15900 / 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→1.95 Å / Total num. of bins used: 20
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