+Open data
-Basic information
Entry | Database: PDB / ID: 6l4n | ||||||
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Title | Domain swapped dimer of Monellin loop1 mutant with QVPAG motif | ||||||
Components | Single chain Monellin | ||||||
Keywords | PLANT PROTEIN / Monomer / L1 mutant | ||||||
Biological species | Dioscoreophyllum cumminsii (serendipity berry) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.431 Å | ||||||
Authors | Manjula, R. / Ramaswamy, S. / Gosavi, S. | ||||||
Citation | Journal: To Be Published Title: Domain swapped dimer of Monellin lopp1 mutant with QVPAG motif Authors: Manjula, R. / Ramaswamy, S. / Gosavi, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l4n.cif.gz | 52.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l4n.ent.gz | 35.9 KB | Display | PDB format |
PDBx/mmJSON format | 6l4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6l4n_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6l4n_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6l4n_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 6l4n_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l4/6l4n ftp://data.pdbj.org/pub/pdb/validation_reports/l4/6l4n | HTTPS FTP |
-Related structure data
Related structure data | 2o9aS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 10546.125 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry) Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | Sequence details | The complete sequence of single chain Monellin has been deposited to NCBI with accession code ...The complete sequence of single chain Monellin has been deposited to NCBI with accession code AFF58925. Residues 48-57 YENEGFREIK | |
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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: 2.33 Å3/Da / Density % sol: 47.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 20% PEG 3350, 200mM Sodium thiocyanate 7.0 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5478 Å | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 21, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5478 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.43→41.872 Å / Num. obs: 7283 / % possible obs: 93.4 % / Redundancy: 2.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.037 / Rrim(I) all: 0.062 / Net I/σ(I): 11.1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2O9A Resolution: 2.431→41.87 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 26.43
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 79.24 Å2 / Biso mean: 35.5651 Å2 / Biso min: 16.48 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.431→41.87 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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