+Open data
-Basic information
Entry | Database: PDB / ID: 6l4j | ||||||
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Title | Monomer structure of monellin loop1 mutant (YEPKG) | ||||||
Components | Single chain Monellin | ||||||
Keywords | PLANT PROTEIN / Single chain Monellin / Loop1 mutant | ||||||
Biological species | Dioscoreophyllum cumminsii (serendipity berry) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Manjula, R. / Ramaswamy, S. / Gosavi, S. | ||||||
Citation | Journal: To Be Published Title: Monomer structure of Loop1 mutant Monellin with YEPKG motif Authors: Manjula, R. / Gosavi, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l4j.cif.gz | 53.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l4j.ent.gz | 36.6 KB | Display | PDB format |
PDBx/mmJSON format | 6l4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6l4j_validation.pdf.gz | 419.4 KB | Display | wwPDB validaton report |
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Full document | 6l4j_full_validation.pdf.gz | 420.6 KB | Display | |
Data in XML | 6l4j_validation.xml.gz | 10 KB | Display | |
Data in CIF | 6l4j_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l4/6l4j ftp://data.pdbj.org/pub/pdb/validation_reports/l4/6l4j | 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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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 2 - 91 / Label seq-ID: 2 - 91
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-Components
#1: Protein | Mass: 10669.255 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry) Production host: Escherichia coli BL21 (bacteria) #2: Water | ChemComp-HOH / | 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: 2.07 Å3/Da / Density % sol: 40.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M carboxylic acid, 0.1M Imidazole, MES monohydrate |
-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 22, 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: 2.3→36.58 Å / Num. obs: 7502 / % possible obs: 96.2 % / Redundancy: 3 % / CC1/2: 0.981 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.052 / Rrim(I) all: 0.091 / Net I/σ(I): 11.5 / Num. measured all: 22730 / Scaling rejects: 104 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3 %
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2O9A Resolution: 2.3→36.579 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 22.51
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 73.83 Å2 / Biso mean: 22.1933 Å2 / Biso min: 7.44 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→36.579 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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