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Yorodumi- PDB-4uop: Crystal structure of the lipoteichoic acid synthase LtaP from Lis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uop | ||||||
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Title | Crystal structure of the lipoteichoic acid synthase LtaP from Listeria monocytogenes | ||||||
Components | LIPOTEICHOIC ACID PRIMASE | ||||||
Keywords | TRANSFERASE / GRAM POSITIVE / CELL WALL | ||||||
Function / homology | Function and homology information sulfuric ester hydrolase activity / membrane => GO:0016020 / extracellular region / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | LISTERIA MONOCYTOGENES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 | 4uop.cif.gz | 186 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uop.ent.gz | 147.3 KB | Display | PDB format |
PDBx/mmJSON format | 4uop.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uop_validation.pdf.gz | 442.8 KB | Display | wwPDB validaton report |
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Full document | 4uop_full_validation.pdf.gz | 444.3 KB | Display | |
Data in XML | 4uop_validation.xml.gz | 33.7 KB | Display | |
Data in CIF | 4uop_validation.cif.gz | 49.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/4uop ftp://data.pdbj.org/pub/pdb/validation_reports/uo/4uop | HTTPS FTP |
-Related structure data
Related structure data | 4uooC 4uorC 2w5qS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 203 - 609 / Label seq-ID: 32 - 438
NCS oper: (Code: given Matrix: (-0.9998, 0.0094, 0.0163), Vector: |
-Components
#1: Protein | Mass: 50679.809 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR CATALYTIC DOMAIN, RESIDUES 193-606 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: Q8Y989, Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups #2: Chemical | #3: Chemical | #4: Chemical | #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: 2.08 Å3/Da / Density % sol: 40.86 % / Description: NONE |
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Crystal grow | pH: 5.4 Details: 100MM NA CACODYLATE PH 5.4, 100MM MGCL2, 33% PEG2000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.28 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→47.96 Å / Num. obs: 77013 / % possible obs: 94.8 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.5 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2W5Q Resolution: 1.75→80.2 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.973 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.117 / 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: 30.899 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→80.2 Å
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Refine LS restraints |
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