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- PDB-5aza: Crystal structure of MBP-sAglB fusion protein with a 20-residue s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5aza | |||||||||
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Title | Crystal structure of MBP-sAglB fusion protein with a 20-residue spacer in the connector helix | |||||||||
![]() | Maltose-binding periplasmic protein,Oligosaccharyl transferase stt3 subunit related protein | |||||||||
![]() | SUGAR BINDING PROTEIN / ![]() ![]() | |||||||||
Function / homology | ![]() dolichyl-phosphooligosaccharide-protein glycotransferase / ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Matsuoka, R. / Kohda, D. | |||||||||
![]() | ![]() Title: Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules. Authors: Matsuoka, R. / Shimada, A. / Komuro, Y. / Sugita, Y. / Kohda, D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 181.2 KB | Display | ![]() |
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PDB format | ![]() | 139.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5az6C ![]() 5az7C ![]() 5az8C ![]() 5az9C ![]() 1anfS ![]() 2zaiS C: citing same article ( S: Starting model for refinement |
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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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Components
#1: Protein | Mass: 97119.969 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 27-394,UNP RESIDUES 491-967 / Mutation: A312V Source method: isolated from a genetically manipulated source Details: The fusion protein of 1-369 Maltose binding protein, 370-389 Linker 390-866 AglB (C-terminal domain, UNP residue 491-967), and 867-872 HisTag Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() Strain: K12 / Gene: malE, b4034, JW3994, PFC_07420 / Production host: ![]() ![]() ![]() |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.08 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 17% PEG 10000, 0.1M Ammounium phosphate, 0.1M Bis-Tris pH5.5, 1.0M Lithium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: May 27, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.08→50 Å / Num. obs: 57642 / % possible obs: 100 % / Redundancy: 12 % / Net I/σ(I): 18.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1ANF, 2ZAI Resolution: 2.08→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.149 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.184 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.58 Å2
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Refinement step | Cycle: LAST / Resolution: 2.08→50 Å
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Refine LS restraints |
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