+Open data
-Basic information
Entry | Database: PDB / ID: 5ej1 | |||||||||
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Title | Pre-translocation state of bacterial cellulose synthase | |||||||||
Components |
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Keywords | METAL BINDING PROTEIN / cellulose biosynthesis / glycosyltransferase / membrane transport | |||||||||
Function / homology | Function and homology information cellulose synthase (UDP-forming) / cellulose synthase (UDP-forming) activity / cellulose biosynthetic process / UDP-glucose metabolic process / cyclic-di-GMP binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Rhodobacter sphaeroides (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.4 Å | |||||||||
Authors | Moragn, J.L.W. / Zimmer, J. | |||||||||
Citation | Journal: Nature / Year: 2016 Title: Observing cellulose biosynthesis and membrane translocation in crystallo. Authors: Morgan, J.L. / McNamara, J.T. / Fischer, M. / Rich, J. / Chen, H.M. / Withers, S.G. / Zimmer, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ej1.cif.gz | 573.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ej1.ent.gz | 479.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ej1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ej1_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 5ej1_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 5ej1_validation.xml.gz | 51.4 KB | Display | |
Data in CIF | 5ej1_validation.cif.gz | 68.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/5ej1 ftp://data.pdbj.org/pub/pdb/validation_reports/ej/5ej1 | 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
-Putative cellulose ... , 2 types, 2 molecules AB
#1: Protein | Mass: 81392.109 Da / Num. of mol.: 1 / Fragment: unp residues 13-740 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158) (bacteria) Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: RSP_0333 / Production host: Escherichia coli (E. coli) References: UniProt: Q3J125, cellulose synthase (UDP-forming) |
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#2: Protein | Mass: 70909.273 Da / Num. of mol.: 1 / Fragment: unp residues 52-720 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158) (bacteria) Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: RSP_0332 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3J126 |
-Protein/peptide / Sugars , 2 types, 2 molecules D
#3: Protein/peptide | Mass: 613.749 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Production host: Escherichia coli (E. coli) |
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#4: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 6 molecules
#5: Chemical | #6: Chemical | #7: Chemical | |
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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: 5.31 Å3/Da / Density % sol: 76.82 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / Details: sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 1 / Detector: CCD / Date: Mar 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→29.5 Å / Num. obs: 86075 / % possible obs: 99.8 % / Redundancy: 6.6 % / Net I/σ(I): 9.6 |
-Processing
Software |
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Refinement | Resolution: 3.4→24.864 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 33.37 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→24.864 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -6.7985 Å / Origin y: 10.5402 Å / Origin z: -58.7582 Å
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Refinement TLS group | Selection details: all |