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Yorodumi- PDB-4uoo: Structure of lipoteichoic acid synthase LtaS from Listeria monocy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uoo | ||||||
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Title | Structure of lipoteichoic acid synthase LtaS from Listeria monocytogenes | ||||||
Components | LIPOTEICHOIC ACID SYNTHASE | ||||||
Keywords | TRANSFERASE / LIPOTEICHOIC ACID SYNTHESIS / CELL WALL / GRAM POSITIVE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | LISTERIA MONOCYTOGENES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Campeotto, I. / Freemont, P. / Grundling, A. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2014 Title: Structural and mechanistic insight into the Listeria monocytogenes two-enzyme lipoteichoic acid synthesis system. Authors: Campeotto, I. / Percy, M.G. / MacDonald, J.T. / Forster, A. / Freemont, P.S. / Grundling, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uoo.cif.gz | 414 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uoo.ent.gz | 339.6 KB | Display | PDB format |
PDBx/mmJSON format | 4uoo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/4uoo ftp://data.pdbj.org/pub/pdb/validation_reports/uo/4uoo | HTTPS FTP |
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-Related structure data
Related structure data | 4uopC 4uorC 2w8dS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 1 / Auth seq-ID: 230 - 644 / Label seq-ID: 36 - 450
NCS oper:
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-Components
#1: Protein | Mass: 52453.633 Da / Num. of mol.: 5 / Fragment: EXTRACELLULAR CATALYTIC DOMAIN, RESIDUES 226-653 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Strain: EGD-E / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA References: UniProt: Q8Y8H6, Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups #2: Chemical | ChemComp-MG / |
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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: 3.5 Å3/Da / Density % sol: 65.28 % / Description: NONE |
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Crystal grow | pH: 4.6 / Details: 0.64M NA ACETATE PH 4.6, 4% PEG3350, 100 MM MGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 29, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 3→106.88 Å / Num. obs: 63877 / % possible obs: 90.7 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.3 / % possible all: 84.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2W8D Resolution: 3→108.88 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.875 / Cross valid method: THROUGHOUT / ESU R Free: 0.431 / 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 mean: 49.48 Å2
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Refinement step | Cycle: LAST / Resolution: 3→108.88 Å
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Refine LS restraints |
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