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Yorodumi- PDB-6x9p: 2-deoxyribose-bound structure of Marinomonas primoryensis PA14 ca... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6x9p | ||||||
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Title | 2-deoxyribose-bound structure of Marinomonas primoryensis PA14 carbohydrate-binding domain | ||||||
Components | Antifreeze protein | ||||||
Keywords | SUGAR BINDING PROTEIN / 2-deoxyribose-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 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 | 6x9p.cif.gz | 143.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x9p.ent.gz | 101.2 KB | Display | PDB format |
PDBx/mmJSON format | 6x9p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6x9p_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6x9p_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6x9p_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 6x9p_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/6x9p ftp://data.pdbj.org/pub/pdb/validation_reports/x9/6x9p | HTTPS FTP |
-Related structure data
Related structure data | 6x7jC 6x7tC 6x7xC 6x7yC 6x7zC 6x8aC 6x8dC 6x8yC 6x95C 6x9mC 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: 20307.580 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: Chemical | ChemComp-UZJ / | ||||||
#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: 2.24 Å3/Da / Density % sol: 44.98 % |
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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-ribose |
-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→39.74 Å / Num. obs: 106580 / % possible obs: 95.76 % / Redundancy: 11.1 % / Biso Wilson estimate: 8.69 Å2 / Rpim(I) all: 0.018 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 0.96→1 Å / Num. unique obs: 7177 / Rpim(I) all: 1.468 |
-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→39.73 Å / SU ML: 0.095 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 11.8735 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: 12.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→39.73 Å
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Refine LS restraints |
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LS refinement shell |
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