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Yorodumi- PDB-6lay: Domain-swapped dimer structure of a Single-chain Monellin loop1-d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lay | ||||||
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Title | Domain-swapped dimer structure of a Single-chain Monellin loop1-delta4-QVVAG mutant | ||||||
Components | Monellin chain B,Monellin chain A | ||||||
Keywords | PLANT PROTEIN / Monomer / L1 mutant | ||||||
Function / homology | Monellin, A chain / Monellin, A chain superfamily / Monellin, B chain / Monellin / Monellin / Cystatin superfamily / Monellin chain A / Monellin chain B Function and homology information | ||||||
Biological species | Dioscoreophyllum cumminsii (serendipity berry) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.001 Å | ||||||
Authors | Manjula, R. / Subramanian, R. / Gosavi, S. | ||||||
Citation | Journal: To Be Published Title: Domain-swapped dimer structure of a Single-chain Monellin loop1-delta4-QVVAG mutant Authors: Manjula, R. / Subramanian, 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 | 6lay.cif.gz | 49.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lay.ent.gz | 34.4 KB | Display | PDB format |
PDBx/mmJSON format | 6lay.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lay_validation.pdf.gz | 425.4 KB | Display | wwPDB validaton report |
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Full document | 6lay_full_validation.pdf.gz | 426.1 KB | Display | |
Data in XML | 6lay_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 6lay_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/6lay ftp://data.pdbj.org/pub/pdb/validation_reports/la/6lay | HTTPS FTP |
-Related structure data
Related structure data | 2o9uS 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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Unit cell |
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-Components
#1: Protein | Mass: 10840.429 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The fusion protein of Monellin chain B, LINKER and Monellin chain A Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry) Production host: Escherichia coli (E. coli) / References: UniProt: P02882, UniProt: P02881 |
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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, hanging drop / pH: 8.5 Details: 20% PEG 3350, 0.2mM sodium acetate ,Tris HCl pH 8.5 |
-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: Apr 8, 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: 3→45.29 Å / Num. obs: 4033 / % possible obs: 100 % / Redundancy: 5.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.047 / Rrim(I) all: 0.109 / Net I/σ(I): 12.5 / Num. measured all: 21231 / Scaling rejects: 6 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2O9U Resolution: 3.001→45.289 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||
Displacement parameters | Biso max: 46.47 Å2 / Biso mean: 32.272 Å2 / Biso min: 21.7 Å2 | ||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.001→45.289 Å
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LS refinement shell | Resolution: 3.001→3.18 Å / Rfactor Rfree error: 0
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