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Yorodumi- PDB-6x95: 2-deoxy-glucose-bound structure of Marinomonas primoryensis PA14 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6x95 | ||||||
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Title | 2-deoxy-glucose-bound structure of Marinomonas primoryensis PA14 carbohydrate-binding domain | ||||||
Components | Antifreeze protein | ||||||
Keywords | SUGAR BINDING PROTEIN / 2-deoxy-glucose-MpPA14 complex / PA14 domain / carbohydrate-binding protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Marinomonas primoryensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Guo, S. / Davies, P.L. | ||||||
Funding support | 1items
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Citation | Journal: Mbio / Year: 2021 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: Journal: To Be Published Title: Molecular basis for a bacterial adhesins sugar-binding module Authors: Guo, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6x95.cif.gz | 93.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x95.ent.gz | 64.4 KB | Display | PDB format |
PDBx/mmJSON format | 6x95.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6x95_validation.pdf.gz | 818.1 KB | Display | wwPDB validaton report |
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Full document | 6x95_full_validation.pdf.gz | 817.8 KB | Display | |
Data in XML | 6x95_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 6x95_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/6x95 ftp://data.pdbj.org/pub/pdb/validation_reports/x9/6x95 | HTTPS FTP |
-Related structure data
Related structure data | 6x7jC 6x7tC 6x7xC 6x7yC 6x7zC 6x8aC 6x8dC 6x8yC 6x9mC 6x9pC 6xa5C 6xacC 6xaqC 5j6yS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20377.607 Da / Num. of mol.: 1 / Fragment: carbohydrate-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Marinomonas primoryensis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A1YIY3 | ||||||
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#2: Sugar | ChemComp-Z61 / | ||||||
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.63 % |
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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) 2-deoxy glucose |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å |
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: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 0.96→42.08 Å / Num. obs: 103370 / % possible obs: 96.25 % / Redundancy: 10.9 % / Biso Wilson estimate: 10.08 Å2 / Rrim(I) all: 0.058 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 0.96→1 Å / Num. unique obs: 7163 / Rpim(I) all: 3.13 / % possible all: 67.7 |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5J6Y Resolution: 1.1→42.08 Å / SU ML: 0.0867 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.5883 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: 14.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→42.08 Å
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Refine LS restraints |
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LS refinement shell |
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