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- PDB-6i0a: Crystal structure of RlpA SPOR domain from Pseudomonas aeruginosa... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6i0a | |||||||||
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Title | Crystal structure of RlpA SPOR domain from Pseudomonas aeruginosa in complex with nuded glycan obtained by co-crystallization | |||||||||
![]() | Endolytic peptidoglycan transglycosylase RlpA | |||||||||
![]() | CELL CYCLE / Lytic transglycosylase / septum / SPOR domain / cell division / divisome / murein / denuded glycan | |||||||||
Function / homology | ![]() Lyases; Carbon-oxygen lyases; Acting on polysaccharides / lytic endotransglycosylase activity / peptidoglycan metabolic process / peptidoglycan binding / cell outer membrane / cell wall organization / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Alcorlo, M. / Hermoso, J.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of denuded glycan recognition by SPOR domains in bacterial cell division. Authors: Alcorlo, M. / Dik, D.A. / De Benedetti, S. / Mahasenan, K.V. / Lee, M. / Dominguez-Gil, T. / Hesek, D. / Lastochkin, E. / Lopez, D. / Boggess, B. / Mobashery, S. / Hermoso, J.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.7 KB | Display | ![]() |
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PDB format | ![]() | 33.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 768.1 KB | Display | ![]() |
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Full document | ![]() | 768.1 KB | Display | |
Data in XML | ![]() | 6.6 KB | Display | |
Data in CIF | ![]() | 8.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6i05SC ![]() 6i09C ![]() 6i0nC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 8173.327 Da / Num. of mol.: 1 / Fragment: SPOR Domain, UNP residues 265-342 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A0A0A8RDC6, UniProt: Q9X6V6*PLUS, Lyases; Carbon-oxygen lyases; Acting on polysaccharides |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.74 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.15 M NaF and 16% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979257 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→48.01 Å / Num. all: 22538 / Num. obs: 272584 / % possible obs: 99.7 % / Redundancy: 12.1 % / Biso Wilson estimate: 17.93 Å2 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.011 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 1.3→1.346 Å / Num. unique obs: 2207 / Rpim(I) all: 0.34 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6I05 Resolution: 1.3→48.01 Å / SU ML: 0.1159 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.4182 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→48.01 Å
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Refine LS restraints |
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LS refinement shell |
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