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Yorodumi- PDB-6gpz: Cell division regulator GpsB in complex with peptide fragment of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gpz | ||||||
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Title | Cell division regulator GpsB in complex with peptide fragment of L. monocytogenes Penicillin Binding Protein PBPA1 | ||||||
Components |
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Keywords | CELL CYCLE / Bacterial cell division regulator / peptidoglycan synthesis regulator / penicillin binding protein interaction partner / protein-peptide complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) Listeria monocytogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Cleverley, R.M. / Lewis, R.J. / Rutter, Z.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: The cell cycle regulator GpsB functions as cytosolic adaptor for multiple cell wall enzymes. Authors: Cleverley, R.M. / Rutter, Z.J. / Rismondo, J. / Corona, F. / Tsui, H.T. / Alatawi, F.A. / Daniel, R.A. / Halbedel, S. / Massidda, O. / Winkler, M.E. / Lewis, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gpz.cif.gz | 70.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gpz.ent.gz | 50.7 KB | Display | PDB format |
PDBx/mmJSON format | 6gpz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/6gpz ftp://data.pdbj.org/pub/pdb/validation_reports/gp/6gpz | HTTPS FTP |
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-Related structure data
Related structure data | 6gp7SC 6gqaC 6gqnC 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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-Components
#1: Protein | Mass: 7610.618 Da / Num. of mol.: 2 / Mutation: K32E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 Gene: gpsB, ypsB, BSU22180 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CI74 #2: Protein/peptide | | Mass: 1855.083 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Listeria monocytogenes (bacteria) #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-IMD / | #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: 1.98 Å3/Da / Density % sol: 37.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M imidazole pH 8, 0.2M zinc acetate, 20% PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→31.42 Å / Num. obs: 17944 / % possible obs: 99.8 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rpim(I) all: 0.044 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 902 / CC1/2: 0.743 / Rpim(I) all: 0.386 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GP7 Resolution: 1.6→29.288 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→29.288 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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