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Yorodumi- PDB-7mg9: Concanavalin A bound to DNA glycoconjugates, Man-TTTT and Man-AAAA -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mg9 | |||||||||
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Title | Concanavalin A bound to DNA glycoconjugates, Man-TTTT and Man-AAAA | |||||||||
Components |
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Keywords | SUGAR BINDING PROTEIN/DNA / Lectin / DNA complex / SUGAR BINDING PROTEIN / SUGAR BINDING PROTEIN-DNA complex | |||||||||
Function / homology | Function and homology information regulation of defense response to virus / D-mannose binding / defense response / metal ion binding Similarity search - Function | |||||||||
Biological species | Canavalia ensiformis (jack bean) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | |||||||||
Authors | Partridge, B.E. / Winegar, P.H. / Mirkin, C.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2021 Title: Redefining Protein Interfaces within Protein Single Crystals with DNA. Authors: Partridge, B.E. / Winegar, P.H. / Han, Z. / Mirkin, C.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mg9.cif.gz | 112.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mg9.ent.gz | 82 KB | Display | PDB format |
PDBx/mmJSON format | 7mg9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/7mg9 ftp://data.pdbj.org/pub/pdb/validation_reports/mg/7mg9 | HTTPS FTP |
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-Related structure data
Related structure data | 7mg1C 7mg2C 7mg3C 7mg4C 7mg5C 7mg6C 7mg7C 7mg8C 7mgaC 7mgbC 7mgcC 7mgdC 5cnaS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 1 - 237 / Label seq-ID: 1 - 237
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-Components
-DNA chain , 2 types, 2 molecules CD
#2: DNA chain | Mass: 1207.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 1171.814 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 25622.385 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P02866 #6: Sugar | |
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-Non-polymers , 4 types, 156 molecules
#4: Chemical | #5: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.2 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Sitting drop comprising 1 uL of Concanavalin A (32 uM), Man-TTTT (64 uM), and Man-AAAA (64 uM) + 1 uL crystallization condition (Helix screen, condition B5: 0.1 M lithium chloride, 0.01 M ...Details: Sitting drop comprising 1 uL of Concanavalin A (32 uM), Man-TTTT (64 uM), and Man-AAAA (64 uM) + 1 uL crystallization condition (Helix screen, condition B5: 0.1 M lithium chloride, 0.01 M manganese(II) chloride tetrahydrate, 0.05 M MES (pH 6.5), 17% w/v PEG 4000). Reservoir contained 70 uL of crystallization condition |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Sep 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→70.18 Å / Num. obs: 17243 / % possible obs: 93.1 % / Redundancy: 3.25 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 5.9147 |
Reflection shell | Resolution: 2.55→2.69 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.58 / Num. unique obs: 2376 / % possible all: 86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CNA Resolution: 2.55→70.18 Å / Cor.coef. Fo:Fc: 0.86 / Cor.coef. Fo:Fc free: 0.794 / SU B: 18.314 / SU ML: 0.376 / Cross valid method: THROUGHOUT / ESU R: 0.892 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.06 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→70.18 Å
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Refine LS restraints |
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