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Yorodumi- PDB-5ycw: Double domain swapped dimer of engineered hairpin loop1 and loop3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ycw | ||||||
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Title | Double domain swapped dimer of engineered hairpin loop1 and loop3 mutant 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 / Cystatin superfamily / Monellin chain B Function and homology information | ||||||
Biological species | Dioscoreophyllum cumminsii (serendipity berry) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.285 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 | 5ycw.cif.gz | 51.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ycw.ent.gz | 35.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ycw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ycw_validation.pdf.gz | 418.8 KB | Display | wwPDB validaton report |
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Full document | 5ycw_full_validation.pdf.gz | 418.7 KB | Display | |
Data in XML | 5ycw_validation.xml.gz | 5.1 KB | Display | |
Data in CIF | 5ycw_validation.cif.gz | 6.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/5ycw ftp://data.pdbj.org/pub/pdb/validation_reports/yc/5ycw | HTTPS FTP |
-Related structure data
Related structure data | 5yctC 5ycuC 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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Unit cell |
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-Components
#1: Protein | Mass: 10622.219 Da / Num. of mol.: 1 Mutation: YENEGFREIK to QVVA in loop1, 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 |
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#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 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.21 % |
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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 6.4-6.8, Crystals grew in a week PH range: 6.4-7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 2.285→41.66 Å / Num. obs: 6521 / % possible obs: 97.28 % / Redundancy: 5.9 % / Biso Wilson estimate: 71.49 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03691 / Net I/σ(I): 22.76 |
Reflection shell | Highest resolution: 2.285 Å / Rmerge(I) obs: 0.7052 / Mean I/σ(I) obs: 2.46 / CC1/2: 0.85 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IV7 Resolution: 2.285→41.66 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.91
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.285→41.66 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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