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Yorodumi- PDB-4uor: Structure of lipoteichoic acid synthase LtaS from Listeria monocy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uor | ||||||
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Title | Structure of lipoteichoic acid synthase LtaS from Listeria monocytogenes in complex with glycerol phosphate | ||||||
Components | LIPOTEICHOIC ACID SYNTHASE | ||||||
Keywords | TRANSFERASE / LIPOTEICHOIC ACID SYNTHESIS / CELL WALL / LTAS / GRAM POSITIVE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | LISTERIA MONOCYTOGENES EGD-E (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.194 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 | 4uor.cif.gz | 968.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uor.ent.gz | 802.3 KB | Display | PDB format |
PDBx/mmJSON format | 4uor.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uor_validation.pdf.gz | 565.9 KB | Display | wwPDB validaton report |
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Full document | 4uor_full_validation.pdf.gz | 593.9 KB | Display | |
Data in XML | 4uor_validation.xml.gz | 184.2 KB | Display | |
Data in CIF | 4uor_validation.cif.gz | 265.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/4uor ftp://data.pdbj.org/pub/pdb/validation_reports/uo/4uor | HTTPS FTP |
-Related structure data
Related structure data | 4uooSC 4uopC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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11 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 52453.633 Da / Num. of mol.: 11 / Fragment: EXTRACELLULAR CATALYTIC DOMAIN, RESIDUES 225-653 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LISTERIA MONOCYTOGENES EGD-E (bacteria) 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 / #3: Chemical | ChemComp-GP9 / ( #4: 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: 3.1 Å3/Da / Density % sol: 60.7 % / Description: NONE |
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Crystal grow | pH: 4.6 / Details: 0.64M NA ACETATE PH 4.6, 4% PEG3350, 100MM MGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Apr 23, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection twin | Operator: K,H,-L / Fraction: 0 |
Reflection | Resolution: 2.2→48.71 Å / Num. obs: 335456 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.7 / % possible all: 95.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4UOO Resolution: 2.194→48.71 Å / σ(F): 0 / Phase error: 19.81 / Stereochemistry target values: TWIN_LSQ_F Details: PHE K 282 AND LYSK 459 ARE C-BETA OUTLIERS. NO DENSITY FOR THESE RESIDUES. TPO307 WAS EXCLUDED FROM NCS IN EACH MONOMER BY PHENIX REFINEMENT WITH REFMAC DETECTS 9 PERCENT TWINNING WITH ...Details: PHE K 282 AND LYSK 459 ARE C-BETA OUTLIERS. NO DENSITY FOR THESE RESIDUES. TPO307 WAS EXCLUDED FROM NCS IN EACH MONOMER BY PHENIX REFINEMENT WITH REFMAC DETECTS 9 PERCENT TWINNING WITH OPERATOR K,H,-L. FINAL REFINEMENT IN PHENIX DOES NOT DETECT ANY TWINNING. THIS DISCREPANCY IS PROBABLY DUE TO THE DISORDER OF MONOMER K.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.194→48.71 Å
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Refine LS restraints |
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LS refinement shell |
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