+Open data
-Basic information
Entry | Database: PDB / ID: 7rms | ||||||
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Title | Crystal structure of [I11G]cycloviolacin O2 | ||||||
Components |
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Keywords | PLANT PROTEIN / cyclic peptides / cyclotides / quasi-racemic | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Viola odorata (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Huang, Y.H. / Du, Q. / Craik, D.J. | ||||||
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: Huang, Y.H. / Du, Q. / Jiang, Z. / King, G.J. / Collins, B.M. / Wang, C.K. / Craik, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rms.cif.gz | 49.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rms.ent.gz | 35.1 KB | Display | PDB format |
PDBx/mmJSON format | 7rms.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rm/7rms ftp://data.pdbj.org/pub/pdb/validation_reports/rm/7rms | HTTPS FTP |
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-Related structure data
Related structure data | 7rmqC 7rmrC 2knmS C: citing same article (ref.) 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/peptide | [ Mass: 3111.664 Da / Num. of mol.: 1 / Mutation: I11G / Source method: obtained synthetically / Source: (synth.) Viola odorata (plant) / References: UniProt: P58434 | ||||||
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#2: Polypeptide(D) | Mass: 3165.756 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Viola odorata (plant) / References: UniProt: P58434 | ||||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | The authors state that chain B is indeed D-peptide and is all-D amino acids. | 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: 1.47 Å3/Da / Density % sol: 16.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium thiocyanate, 27% (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: 0.9641 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9641 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→26.96 Å / Num. obs: 14958 / % possible obs: 99.61 % / Redundancy: 2 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.01621 / Net I/σ(I): 9.76 |
Reflection shell | Resolution: 1.1→1.139 Å / Num. unique obs: 1474 / CC1/2: 0.996 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2KNM Resolution: 1.1→24.11 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 19.63 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→24.11 Å
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Refine LS restraints |
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LS refinement shell |
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