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- PDB-5c7r: Revealing surface waters on an antifreeze protein by fusion prote... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5c7r | |||||||||
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Title | Revealing surface waters on an antifreeze protein by fusion protein crystallography | |||||||||
![]() | Fusion protein of Maltose-binding periplasmic protein and Type-3 ice-structuring protein HPLC 12 | |||||||||
![]() | ANTIFREEZE PROTEIN / fusion protein | |||||||||
Function / homology | ![]() 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 ...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 | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Sun, T. / Gauthier, S. / Campbell, R.L. / Davies, P.L. | |||||||||
![]() | ![]() Title: Revealing Surface Waters on an Antifreeze Protein by Fusion Protein Crystallography Combined with Molecular Dynamic Simulations. Authors: Sun, T. / Gauthier, S.Y. / Campbell, R.L. / Davies, P.L. #1: ![]() Title: Understanding the mechanism of ice binding by type III antifreeze proteins. Authors: Antson, A.A. / Smith, D.J. / Roper, D.I. / Lewis, S. / Caves, L.S. / Verma, C.S. / Buckley, S.L. / Lillford, P.J. / Hubbard, R.E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 195.6 KB | Display | ![]() |
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PDB format | ![]() | 154.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 36.2 KB | Display | |
Data in CIF | ![]() | 54.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 48512.152 Da / Num. of mol.: 2 Fragment: UNP P0AEY0 residues 27-384, UNP P19614 residues 1-63 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: malE, Z5632, ECs5017 / Production host: ![]() ![]() References: UniProt: P0AEY0, UniProt: P19614, UniProt: P0AEX9*PLUS #2: Polysaccharide | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4 / Details: 1.75 M (NH4)2SO4, 100 mM NaOAC (pH 4.4) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 9, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→48.2 Å / Num. obs: 72126 / % possible obs: 96.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 9.36 |
Reflection shell | Resolution: 1.94→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.362 / Mean I/σ(I) obs: 1.1 / % possible all: 86.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1HG7,3G7W Resolution: 1.94→48.158 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 24.76 / 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: 1.94→48.158 Å
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Refine LS restraints |
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LS refinement shell |
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