+Open data
-Basic information
Entry | Database: PDB / ID: 6s3f | ||||||
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Title | Moringa seed protein Mo-CBP3-4 | ||||||
Components | (2S albuminPlant lipid transfer proteins) x 2 | ||||||
Keywords | ANTIFUNGAL PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Moringa oleifera (horseradish tree) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.68 Å | ||||||
Authors | Moulin, M. / Mossou, E. / Mitchell, E.P. / Haertlein, M. / Forsyth, V.T. / Rennie, A.R. | ||||||
Citation | Journal: J Colloid Interface Sci / Year: 2019 Title: Towards a molecular understanding of the water purification properties of Moringa seed proteins. Authors: Moulin, M. / Mossou, E. / Signor, L. / Kieffer-Jaquinod, S. / Kwaambwa, H.M. / Nermark, F. / Gutfreund, P. / Mitchell, E.P. / Haertlein, M. / Forsyth, V.T. / Rennie, A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6s3f.cif.gz | 30.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s3f.ent.gz | 22.7 KB | Display | PDB format |
PDBx/mmJSON format | 6s3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/6s3f ftp://data.pdbj.org/pub/pdb/validation_reports/s3/6s3f | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 7374.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Moringa oleifera (horseradish tree) / References: UniProt: W5S2D2 |
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#2: Protein/peptide | Mass: 3248.731 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Moringa oleifera (horseradish tree) / References: UniProt: W5S2D2 |
-Non-polymers , 4 types, 51 molecules
#3: Chemical | ChemComp-CL / | ||||
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#4: Chemical | ChemComp-FMT / #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1M citic acid 2.4M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 16, 2013 |
Radiation | Monochromator: silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→54.45 Å / Num. obs: 15156 / % possible obs: 99.6 % / Redundancy: 7.1 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.02 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 1.68→1.71 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 741 / Rpim(I) all: 0.411 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.68→19.37 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.803 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.1 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.791 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→19.37 Å
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Refine LS restraints |
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