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Yorodumi- PDB-6slc: Mutations in SsgB correlate to longitudinal cell division during ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6slc | ||||||
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Title | Mutations in SsgB correlate to longitudinal cell division during sporulation of Streptomyces coelicolor | ||||||
Components | Sporulation and cell division protein SsgA | ||||||
Keywords | CELL CYCLE / beta barrel / anti-parallel beta-sheet interfaces / cell division component | ||||||
Function / homology | Sporulation-specific cell division protein SsgB / Sporulation-specific cell division protein SsgB superfamily / Streptomyces sporulation and cell division protein, SsgA / cell septum / sporulation resulting in formation of a cellular spore / cell division / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Sporulation and cell division protein SsgA Function and homology information | ||||||
Biological species | Streptomyces sp. Ag82_O1-9 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Xiao, X.S. / Willemse, J. | ||||||
Citation | Journal: Open Biology / Year: 2021 Title: Ectopic positioning of the cell division plane is associated with single amino acid substitutions in the FtsZ-recruiting SsgB in Streptomyces . Authors: Xiao, X. / Willemse, J. / Voskamp, P. / Li, X. / Prota, A.E. / Lamers, M. / Pannu, N. / Abrahams, J.P. / van Wezel, G.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6slc.cif.gz | 95.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6slc.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6slc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sl/6slc ftp://data.pdbj.org/pub/pdb/validation_reports/sl/6slc | HTTPS FTP |
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-Related structure data
Related structure data | 3cm1S 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 ensembles :
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-Components
#1: Protein | Mass: 17053.934 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. Ag82_O1-9 (bacteria) / Gene: BX279_7474 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3D9WLS9 #2: Chemical | ChemComp-PEG / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.98 Å3/Da / Density % sol: 69.09 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Sodium chloride, 0.1 M Sodium/potassium phosphate (pH 6.2), 50% PEG200 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.975 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2017 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→109.927 Å / Num. obs: 33694 / % possible obs: 95.5 % / Redundancy: 4 % / Biso Wilson estimate: 47.9 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.037 / Rrim(I) all: 0.076 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.27→2.309 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.009 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1579 / CC1/2: 0.477 / Rpim(I) all: 0.57 / Rrim(I) all: 1.167 / % possible all: 92.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CM1 Resolution: 2.3→49.213 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.243 / WRfactor Rwork: 0.195 / SU B: 9.749 / SU ML: 0.211 / Average fsc free: 0.7772 / Average fsc work: 0.79 / Cross valid method: FREE R-VALUE / ESU R: 0.239 / ESU R Free: 0.211 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.539 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→49.213 Å
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Refine LS restraints |
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LS refinement shell |
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