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- PDB-2vfo: Low Temperature Structure of P22 Tailspike Protein Fragment (109-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vfo | ||||||
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Title | Low Temperature Structure of P22 Tailspike Protein Fragment (109-666), Mutant V125L | ||||||
![]() | P22 TAILSPIKE PROTEIN, MUTANT V125L | ||||||
![]() | HYDROLASE / P22 TAILSPIKE PROTEIN / SALMONELLA BACTERIOPHAGE P22 / PROTEIN FOLDING / PROTEIN STABILITY / RIGHT-HANDED PARALLEL BETA-HELIX / LATE PROTEIN / ENDOGLYCOSIDASE | ||||||
Function / homology | ![]() endo-1,3-alpha-L-rhamnosidase activity / symbiont entry into host cell via disruption of host cell envelope lipopolysaccharide / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / symbiont entry into host / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / adhesion receptor-mediated virion attachment to host cell / metabolic process / virion attachment to host cell Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Becker, M. / Mueller, J.J. / Heinemann, U. / Seckler, R. | ||||||
![]() | ![]() Title: Side-Chain Stacking and Beta-Helix Stability in P22 Tailspike Protein Authors: Becker, M. / Mueller, J.J. / Weikl, T. / Heinemann, U. / Seckler, R. #1: ![]() Title: Plasticity and Steric Strain in a Parallel Beta-Helix: Rational Mutations in the P22 Tailspike Protein Authors: Schuler, B. / Fuerst, F. / Osterroth, F. / Steinbacher, S. / Huber, R. / Seckler, R. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 147.2 KB | Display | ![]() |
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PDB format | ![]() | 113.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.3 KB | Display | ![]() |
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Full document | ![]() | 455.5 KB | Display | |
Data in XML | ![]() | 30.3 KB | Display | |
Data in CIF | ![]() | 48.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vfmC ![]() 2vfnC ![]() 2vfpC ![]() 2vfqC ![]() 1tyvS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 60247.316 Da / Num. of mol.: 1 / Fragment: RESIDUES 110-667 / Mutation: YES Source method: isolated from a genetically manipulated source Details: THE PROTEIN IS LACKING THE N-TERMINAL HEAD-BINDING DOMAIN Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P12528, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds | ||||||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | GLY513 IN THE SWISSPROT ENTRY WAS CORRECTED IN THE SEQUENCE TO SER513 WHICH IS ALSO PRESENT IN THE ...GLY513 IN THE SWISSPROT ENTRY WAS CORRECTED IN THE SEQUENCE TO SER513 WHICH IS ALSO PRESENT IN THE PARENT WILD-TYPE DNA | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.2 % Description: FOR REFINEMENT REFLECTIONS IN THE CORNERS OF THE IMAGE PLATE WERE USED ADDITIONALLY, 1.5-1.59 A RESOLUTION, COMPETENESS 40.4 PERCENT, REDUNDANCY 1.7, RSYM 0.123, I DIVIDED BY SIGMA(I) 5.3 |
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Crystal grow | pH: 10 Details: DROP: 2 MICROLITER 1.5 M AMMONIUM SULFATE, 0.1 M SODIUM PHOSPHATE, PH 10.0, PLUS 3.3 MICROLITER 10 MG/ML PROTEIN SOLUTION IN 10 MM HEPES, PH 7.0; RESERVOIR: 750 MICOLITER 1.0 M AMMONIUM ...Details: DROP: 2 MICROLITER 1.5 M AMMONIUM SULFATE, 0.1 M SODIUM PHOSPHATE, PH 10.0, PLUS 3.3 MICROLITER 10 MG/ML PROTEIN SOLUTION IN 10 MM HEPES, PH 7.0; RESERVOIR: 750 MICOLITER 1.0 M AMMONIUM SULFATE, 0.1 M SODIUM PHOSPHATE, PH 10.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 29, 2006 / Details: MIRRORS |
Radiation | Monochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92018 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→50 Å / Num. obs: 76307 / % possible obs: 98.1 % / Redundancy: 9.3 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 32.2 |
Reflection shell | Resolution: 1.59→1.7 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 8.9 / % possible all: 90.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1TYV Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.827 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
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Refine LS restraints |
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