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- PDB-6tgf: Pantoea stewartii WceF is a glycan biofilm modifying enzyme with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tgf | ||||||
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Title | Pantoea stewartii WceF is a glycan biofilm modifying enzyme with a bacteriophage tailspike-like parallel beta-helix fold | ||||||
![]() | Exopolysaccharide biosynthesis protein | ||||||
![]() | HYDROLASE / WceF / beta-helix / tailspike-like | ||||||
Function / homology | Bacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding / Pectin lyase fold/virulence factor / : / Amylovoran biosynthesis protein AmsF![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Irmscher, T. / Roske, Y. / Gayk, I. / Heinemann, U. / Barbirz, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Pantoea stewartii WceF is a glycan biofilm-modifying enzyme with a bacteriophage tailspike-like fold. Authors: Irmscher, T. / Roske, Y. / Gayk, I. / Dunsing, V. / Chiantia, S. / Heinemann, U. / Barbirz, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 777.7 KB | Display | ![]() |
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PDB format | ![]() | 646.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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Components
#1: Protein | Mass: 80510.883 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: wceF, CKS_2251 / Plasmid: pET23a / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 52.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20% PEG3350, 0.2M Di-NH4-hydrogen-citrate pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 22, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→48.6 Å / Num. obs: 74949 / % possible obs: 96.4 % / Redundancy: 3.82 % / CC1/2: 0.985 / Rrim(I) all: 0.0231 / Net I/σ(I): 6.77 |
Reflection shell | Resolution: 2.55→2.7 Å / Mean I/σ(I) obs: 1.02 / Num. unique obs: 10202 / CC1/2: 0.36 / Rrim(I) all: 0.1281 / % possible all: 81.4 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 797.42 Å2 / Biso mean: 44.855 Å2 / Biso min: 16.21 Å2
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Refinement step | Cycle: final / Resolution: 2.55→48.6 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 9511 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.55→2.615 Å / Rfactor Rfree error: 0
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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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