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Yorodumi- PDB-7un2: Crystal structure of a lectin from Canavalia maritima seed (ConM)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7un2 | ||||||
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Title | Crystal structure of a lectin from Canavalia maritima seed (ConM) complexed with Indole-3-butyric acid | ||||||
Components | ConM | ||||||
Keywords | SUGAR BINDING PROTEIN / Lectin / ConM / Auxin / Indole-3-butyric acid | ||||||
Function / homology | 3-INDOLEBUTYRIC ACID / D-ALPHA-AMINOBUTYRIC ACID / : Function and homology information | ||||||
Biological species | Canavalia rosea (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | de Sousa, J.P. / Bezerra, E.H.S. / Sales, M.V. / Queiroz, P.P. / da Silva, F.M.S. / Carvalho, C.P.S. / Freire, V.N. / Rocha, B.A.M. | ||||||
Funding support | Brazil, 1items
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Citation | Journal: To Be Published Title: Structural analysis of Canavalia maritima lectin complexed with auxins Authors: de Sousa, J.P. / Bezerra, E.H.S. / Sales, M.V. / Queiroz, P.P. / da Silva, F.M.S. / Carvalho, C.P.S. / Freire, V.N. / Rocha, B.A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7un2.cif.gz | 138.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7un2.ent.gz | 85.4 KB | Display | PDB format |
PDBx/mmJSON format | 7un2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/7un2 ftp://data.pdbj.org/pub/pdb/validation_reports/un/7un2 | HTTPS FTP |
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-Related structure data
Related structure data | 7uodC 2cy6S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 25494.195 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Canavalia rosea (plant) |
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-Non-polymers , 7 types, 359 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-3IB / | #6: Chemical | #7: Chemical | ChemComp-DBB / | #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: 2.37 Å3/Da / Density % sol: 48.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES pH 7.5, 4% PEG 400, 2.0 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.458 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→33.99 Å / Num. obs: 45553 / % possible obs: 99.72 % / Redundancy: 2 % / Biso Wilson estimate: 20.09 Å2 / CC1/2: 1 / Net I/σ(I): 27.87 |
Reflection shell | Resolution: 1.8→1.864 Å / Redundancy: 2 % / Mean I/σ(I) obs: 4.58 / Num. unique obs: 4472 / CC1/2: 0.961 / % possible all: 99.78 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CY6 Resolution: 1.8→33.99 Å / SU ML: 0.1977 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3111 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: 26.74 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→33.99 Å
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Refine LS restraints |
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LS refinement shell |
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