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Yorodumi- PDB-4wjt: Stationary Phase Survival Protein YuiC from B.subtilis complexed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wjt | ||||||
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Title | Stationary Phase Survival Protein YuiC from B.subtilis complexed with NAG | ||||||
Components | Uncharacterized protein YuiC | ||||||
Keywords | LYASE / lytic transglycosylase / peptidoglycan remodelling / stationary phase / MltA | ||||||
Function / homology | 3D domain / 3D domain / RlpA-like domain superfamily / peptidoglycan turnover / outer membrane / hydrolase activity, hydrolyzing O-glycosyl compounds / Chem-3P9 / Uncharacterized protein YuiC Function and homology information | ||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å | ||||||
Authors | Quay, D.H.X. / Cole, A.R. / Cryar, A. / Thalassinos, K. / Williams, M.A. / Bhakta, S. / Keep, N.H. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Bmc Struct.Biol. / Year: 2015 Title: Structure of the stationary phase survival protein YuiC from B.subtilis. Authors: Quay, D.H. / Cole, A.R. / Cryar, A. / Thalassinos, K. / Williams, M.A. / Bhakta, S. / Keep, N.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wjt.cif.gz | 151.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wjt.ent.gz | 119 KB | Display | PDB format |
PDBx/mmJSON format | 4wjt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/4wjt ftp://data.pdbj.org/pub/pdb/validation_reports/wj/4wjt | HTTPS FTP |
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-Related structure data
Related structure data | 4wliC 4wlkC 2ae0S 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 72 - 217 / Label seq-ID: 21 - 166
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-Components
#1: Protein | Mass: 18606.896 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Gene: yuiC, BSU32070 / Plasmid: pNic28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta-2 / References: UniProt: O32108 #2: Sugar | #3: Chemical | ChemComp-DMS / #4: Chemical | ChemComp-3P9 / ( | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.57 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 5mM NAG, 48% (v/v) polypropylene glycol P400, 0.1M HEPES pH 6, 3% (v/v) DMSO |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.21→36.37 Å / Num. all: 89967 / Num. obs: 89967 / % possible obs: 98.8 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.21→1.23 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 2.4 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ae0 Resolution: 1.21→72.74 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.097 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.032 / 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: 23.243 Å2
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Refinement step | Cycle: 1 / Resolution: 1.21→72.74 Å
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Refine LS restraints |
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