+Open data
-Basic information
Entry | Database: PDB / ID: 7rih | ||||||
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Title | hyen D | ||||||
Components |
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Keywords | PLANT PROTEIN / Cytotoxicity / cyclotides / quasi-racemic crystallography | ||||||
Function / homology | Function and homology information hemolysis in another organism / cytolysis in another organism / defense response Similarity search - Function | ||||||
Biological species | Hybanthus enneaspermus (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Du, Q. / Huang, Y.H. / Craik, D.J. / Wang, C.K. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Molecules / Year: 2021 Title: Enabling efficient folding and high-resolution crystallographic analysis of bracelet cyclotides Authors: Craik, D.J. / Huang, Y.H. / Wang, C.K. / Du, Q. / King, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rih.cif.gz | 52 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rih.ent.gz | 37.6 KB | Display | PDB format |
PDBx/mmJSON format | 7rih.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/7rih ftp://data.pdbj.org/pub/pdb/validation_reports/ri/7rih | HTTPS FTP |
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-Related structure data
Related structure data | 7riiSC 7rijC 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: Polypeptide(D) | Mass: 3179.757 Da / Num. of mol.: 1 / Mutation: I11L / Source method: obtained synthetically / Source: (synth.) Hybanthus enneaspermus (plant) | ||||
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#2: Protein/peptide | Mass: 3182.778 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hybanthus enneaspermus (plant) / References: UniProt: C0HLN8 | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.72 Å3/Da / Density % sol: 28.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.07 M citrate (pH 2.3), 0.03 M Bis-tris propane (pH 9.7) and 16% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95366 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 7, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95366 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→19.98 Å / Num. obs: 9116 / % possible obs: 93.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.03263 / Rrim(I) all: 0.06025 / Net I/σ(I): 13.11 |
Reflection shell | Resolution: 1.35→1.39 Å / Num. unique obs: 507 / CC1/2: 0.998 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7RII Resolution: 1.35→19.98 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 27.16 / 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: 36.84 Å2 / Biso mean: 13.5378 Å2 / Biso min: 6.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.35→19.98 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS params. | Method: refined / Origin x: -6.3242 Å / Origin y: -5.9358 Å / Origin z: 2.5514 Å
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Refinement TLS group |
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