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- PDB-5cbn: Fusion protein of mbp3-16 and B4 domain of protein A from staphyl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5cbn | ||||||
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Title | Fusion protein of mbp3-16 and B4 domain of protein A from staphylococcal aureus with chemical cross-linker EY-CBS | ||||||
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![]() | PROTEIN BINDING / Fusion / EY-CBS / alpha helix / cross-linker | ||||||
Function / homology | ![]() IgG binding / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex ...IgG binding / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / extracellular region / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Jeong, W.H. / Lee, H. / Song, D.H. / Lee, J.O. | ||||||
![]() | ![]() Title: Connecting two proteins using a fusion alpha helix stabilized by a chemical cross linker. Authors: Jeong, W.H. / Lee, H. / Song, D.H. / Eom, J.H. / Kim, S.C. / Lee, H.S. / Lee, H. / Lee, J.O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 227.9 KB | Display | ![]() |
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PDB format | ![]() | 179.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 729.1 KB | Display | ![]() |
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Full document | ![]() | 736.2 KB | Display | |
Data in XML | ![]() | 21.7 KB | Display | |
Data in CIF | ![]() | 30.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5cboC ![]() 5cocC ![]() 5ewxC ![]() 1svxS 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: 40571.961 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 31-392 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: malE, b4034, JW3994 / Production host: ![]() ![]() |
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#2: Antibody | Mass: 19115.420 Da / Num. of mol.: 1 / Fragment: B4 domain (UNP RESIDUES 218-269) / Mutation: E126A, N129A, E133C, G147A Source method: isolated from a genetically manipulated source Details: Fusion protein of mbp3-16 and B4 domain (UNP RESIDUES 102-153) of protein A Source: (gene. exp.) synthetic construct (others), (gene. exp.) ![]() ![]() Gene: spa / Production host: ![]() ![]() |
#3: Chemical | ChemComp-EYC / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.17 % / Description: needle-rod |
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Crystal grow | Temperature: 277 K / Method: evaporation / pH: 6.5 Details: 36% w/v PEG 2000, 0.2M magnesium chloride hexahydrate |
-Data collection
Diffraction | Mean temperature: 77 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 18, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 24863 / % possible obs: 99.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.063 / Χ2: 1.659 / Net I/av σ(I): 38.569 / Net I/σ(I): 15.5 / Num. measured all: 167724 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1SVX Resolution: 2.3→42.085 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.78 / 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: 2.3→42.085 Å
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Refine LS restraints |
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LS refinement shell |
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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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