+Open data
-Basic information
Entry | Database: PDB / ID: 5yct | ||||||
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Title | Engineered hairpin loop3 mutant monomer in Single-chain Monellin | ||||||
Components | Single chain Monellin | ||||||
Keywords | PLANT PROTEIN / domain swapped dimer / Single-chain Monellin / loop mutation / QVVAG motif | ||||||
Function / homology | Monellin, B chain / Monellin / Monellin / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Monellin chain B Function and homology information | ||||||
Biological species | Dioscoreophyllum cumminsii (serendipity berry) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.851 Å | ||||||
Authors | Surana, P. / Nandwani, N. / Udgaonkar, J.B. / Gosavi, S. / Das, R. | ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: A five-residue motif for the design of domain swapping in proteins. Authors: Nandwani, N. / Surana, P. / Negi, H. / Mascarenhas, N.M. / Udgaonkar, J.B. / Das, 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 | 5yct.cif.gz | 92.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yct.ent.gz | 69.6 KB | Display | PDB format |
PDBx/mmJSON format | 5yct.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yct_validation.pdf.gz | 441.1 KB | Display | wwPDB validaton report |
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Full document | 5yct_full_validation.pdf.gz | 443.7 KB | Display | |
Data in XML | 5yct_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 5yct_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/5yct ftp://data.pdbj.org/pub/pdb/validation_reports/yc/5yct | HTTPS FTP |
-Related structure data
Related structure data | 5ycuC 5ycwC 6iwjC 1iv7S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11493.126 Da / Num. of mol.: 2 / Mutation: DYKTR to QVVAG in loop3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry) Production host: Escherichia coli (E. coli) / References: UniProt: P02882*PLUS #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 79-83 DYKTR have been replaced with QVVAG in this structure. C-terminal residues STP are from expression tag. | |
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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: 2.27 Å3/Da / Density % sol: 45.81 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 8-12% (wt/vol) PEG 8000, 50mM sodium phosphate, pH 6.4-7.2, Crystals grew to maximum size in 4-5 days PH range: 6.4-7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.851→24.052 Å / Num. obs: 17514 / % possible obs: 98.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 32.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.017 / Net I/σ(I): 24 |
Reflection shell | Highest resolution: 1.851 Å / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 3.1 / CC1/2: 0.924 / % possible all: 89.04 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IV7 Resolution: 1.851→24.052 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.93
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.851→24.052 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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