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- PDB-6x7y: N-acetyl-glucosamine-bound structure of Marinomonas primoryensis ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6x7y | ||||||
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Title | N-acetyl-glucosamine-bound structure of Marinomonas primoryensis PA14 carbohydrate-binding domain | ||||||
![]() | Antifreeze protein | ||||||
![]() | SUGAR BINDING PROTEIN / N-acetyl-glucosamine-MpPA14 complex / PA14 domain / carbohydrate-binding protein | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guo, S. / Davies, P.L. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural Basis of Ligand Selectivity by a Bacterial Adhesin Lectin Involved in Multispecies Biofilm Formation. Authors: Guo, S. / Vance, T.D.R. / Zahiri, H. / Eves, R. / Stevens, C. / Hehemann, J.H. / Vidal-Melgosa, S. / Davies, P.L. #1: ![]() Title: Molecular basis for a bacterial adhesins sugar-binding module Authors: Guo, 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 | ![]() | 139.3 KB | Display | ![]() |
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PDB format | ![]() | 97.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1010.9 KB | Display | ![]() |
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Full document | ![]() | 1011.8 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 17.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6x7jC ![]() 6x7tC ![]() 6x7xC ![]() 6x7zC ![]() 6x8aC ![]() 6x8dC ![]() 6x8yC ![]() 6x95C ![]() 6x9mC ![]() 6x9pC ![]() 6xa5C ![]() 6xacC ![]() 6xaqC ![]() 5j6yS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 19459.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 2 types, 2 molecules ![](data/chem/img/NDG.gif)
![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#2: Sugar | ChemComp-NDG / |
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#3: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 258 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CA / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.39 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 7 Details: 0.2 M calcium chloride, 0.1 M HEPES (pH 7), 20% (v/v) polyethylene glycol 3350 and ~ 30 % (w/v) N-acetyl-glucosamine |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9615 Å / Relative weight: 1 |
Reflection | Resolution: 0.96→39.71 Å / Num. obs: 106951 / % possible obs: 95.6 % / Redundancy: 11.1 % / Biso Wilson estimate: 7.25 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 22.14 |
Reflection shell | Resolution: 0.96→1.03 Å / Rmerge(I) obs: 1.035 / Num. unique obs: 7708 |
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Processing
Software | Name: PHENIX / Version: 1.17.1_3660 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 5j6y Resolution: 1→39.71 Å / SU ML: 0.0797 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 10.5223 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→39.71 Å
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Refine LS restraints |
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LS refinement shell |
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