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Yorodumi- PDB-6v7g: Binding of Benzoic Acid and Anions Within the Cupin Domains of th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v7g | |||||||||
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Title | Binding of Benzoic Acid and Anions Within the Cupin Domains of the Vicillin Protein Canavalin from Jack Bean (canavalia ensiformis): Crystal Structures | |||||||||
Components | Canavalin | |||||||||
Keywords | PLANT PROTEIN / plant proteins / ligands / salicylic acid / enzymes | |||||||||
Function / homology | Function and homology information nutrient reservoir activity / protein-containing complex / identical protein binding Similarity search - Function | |||||||||
Biological species | Canavalia ensiformis (jack bean) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | |||||||||
Authors | McPherson, A. | |||||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2020 Title: Binding of benzoic acid and anions within the cupin domains of the vicilin protein canavalin from jack bean (Canavalia ensiformis): Crystal structures. Authors: McPherson, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v7g.cif.gz | 225.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v7g.ent.gz | 184.6 KB | Display | PDB format |
PDBx/mmJSON format | 6v7g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/6v7g ftp://data.pdbj.org/pub/pdb/validation_reports/v7/6v7g | HTTPS FTP |
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-Related structure data
Related structure data | 6v7jC 6v7lC 6cb4 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: 50431.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P50477 |
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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-BEZ / |
#4: Chemical | ChemComp-CIT / |
#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: 2.3 Å3/Da / Density % sol: 46 % / Description: short hexagonal prisms |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Vapor diffusion in sitting drop Cryschem plates. Reservoirs were 1.0 M sodium citrate titrated with acetic acid to pH6.0. Drops were initially equal amounts of the reservoir solution with a ...Details: Vapor diffusion in sitting drop Cryschem plates. Reservoirs were 1.0 M sodium citrate titrated with acetic acid to pH6.0. Drops were initially equal amounts of the reservoir solution with a protein stock solution of 30 mg/ml canavalin in water with a trace of ammonium hydroxide. At room temperature crystallization time was about three weeks. PH range: 5.8 - 6.5 |
-Data collection
Diffraction | Mean temperature: 173 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Jun 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→109 Å / Num. obs: 86853 / % possible obs: 99.6 % / Redundancy: 61 % / Biso Wilson estimate: 14.6 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.258 / Rpim(I) all: 0.029 / Rrim(I) all: 0.26 / Rsym value: 0.248 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.4→1.43 Å / Redundancy: 11.8 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3978 / CC1/2: 0.182 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6CB4 6cb4 Resolution: 1.4→109 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.607 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.053 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.09 Å2 / Biso mean: 28.707 Å2 / Biso min: 15.02 Å2
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Refinement step | Cycle: final / Resolution: 1.4→109 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 21.2274 Å / Origin y: 151.639 Å / Origin z: 1.1447 Å
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