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Yorodumi- PDB-5olt: Crystal structure of the extramembrane domain of the cellulose bi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5olt | |||||||||
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Title | Crystal structure of the extramembrane domain of the cellulose biosynthetic protein BcsG from Salmonella typhimurium | |||||||||
Components | Cellulose biosynthesis protein BcsG | |||||||||
Keywords | TRANSFERASE / Cellulose biosynthesis / biofilm / metalloenzyme / alkaline phosphatase family | |||||||||
Function / homology | Cellulose biosynthesis protein BcsG / Cellulose biosynthesis protein BcsG / cellulose biosynthetic process / plasma membrane / CITRIC ACID / Cellulose biosynthesis protein BcsG Function and homology information | |||||||||
Biological species | Salmonella typhimurium LT2 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å | |||||||||
Authors | Vella, P. / Polyakova, A. / Lindqvist, Y. / Schnell, R. / Bourenkov, G. / Schneider, T. / Schneider, G. | |||||||||
Funding support | Sweden, Germany, 2items
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Citation | Journal: J. Mol. Biol. / Year: 2018 Title: Structural and Functional Characterization of the BcsG Subunit of the Cellulose Synthase in Salmonella typhimurium. Authors: Sun, L. / Vella, P. / Schnell, R. / Polyakova, A. / Bourenkov, G. / Li, F. / Cimdins, A. / Schneider, T.R. / Lindqvist, Y. / Galperin, M.Y. / Schneider, G. / Romling, U. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5olt.cif.gz | 182.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5olt.ent.gz | 150 KB | Display | PDB format |
PDBx/mmJSON format | 5olt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5olt_validation.pdf.gz | 450.2 KB | Display | wwPDB validaton report |
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Full document | 5olt_full_validation.pdf.gz | 451.1 KB | Display | |
Data in XML | 5olt_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 5olt_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/5olt ftp://data.pdbj.org/pub/pdb/validation_reports/ol/5olt | HTTPS FTP |
-Related structure data
-Links
-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: 42130.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium LT2 (bacteria) / Gene: bcsG, STM3624 / Production host: Escherichia coli DH5[alpha] / References: UniProt: Q7CPI7 | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.5 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: ammonium citrate, ZnCl2 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.2782 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2782 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→69.85 Å / Num. obs: 60090 / % possible obs: 96.1 % / Redundancy: 9 % / Biso Wilson estimate: 9.8 Å2 / Rpim(I) all: 0.023 / Rsym value: 0.068 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 5 / Num. unique obs: 8728 / Rpim(I) all: 0.206 / Rsym value: 0.538 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.45→69.85 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.814 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.057 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.032 Å2
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Refinement step | Cycle: 1 / Resolution: 1.45→69.85 Å
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Refine LS restraints |
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