+Open data
-Basic information
Entry | Database: PDB / ID: 3fid | ||||||
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Title | LpxR from Salmonella typhimurium | ||||||
Components | Putative outer membrane protein (LpxR) | ||||||
Keywords | MEMBRANE PROTEIN / lipopolysaccharide-modifying outer membrane enzyme | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD, direct methodMULTI using P21212, P2 crystal / Resolution: 1.9 Å | ||||||
Authors | Rutten, L. / Gros, P. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Active-site architecture and catalytic mechanism of the lipid A deacylase LpxR of Salmonella typhimurium Authors: Rutten, L. / Mannie, J.-P.B.A. / Stead, C.M. / Raetz, C.R.H. / Reynolds, C.M. / Bonvin, A.M.J.J. / Tommassen, J.P. / Egmond, M.R. / Trent, M.S. / Gros, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fid.cif.gz | 137.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fid.ent.gz | 109 KB | Display | PDB format |
PDBx/mmJSON format | 3fid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/3fid ftp://data.pdbj.org/pub/pdb/validation_reports/fi/3fid | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32419.988 Da / Num. of mol.: 2 / Fragment: mature domain, UNP residues 24-319 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: strain LT2 / Gene: lpxr / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3) / References: UniProt: Q8ZPT3 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-CXE / #5: 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: 3.19 Å3/Da / Density % sol: 61.47 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 8.5 Details: 14% PEG 6000 (w/v), 10% glycerol (v/v), 50mM Tris-HCl, 5mM zinc chloride, pH 8.5, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 13, 2007 / Details: Toroidal mirror |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.74 Å / Num. all: 66242 / Num. obs: 66190 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.9 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.159 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 15 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 3.6 / Num. unique all: 9516 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD, direct methodMULTI using P21212, P2 crystal Resolution: 1.9→48.74 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.714 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.129 / ESU R Free: 0.127 / 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: 17.925 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→48.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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