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- PDB-7rmr: Crystal structure of [I11L]cycloviolacin O2 -

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Basic information

Entry
Database: PDB / ID: 7rmr
TitleCrystal structure of [I11L]cycloviolacin O2
Components
  • D-[I11L]cycloviolacin O2
  • [I11L]cycloviolacin O2
KeywordsPLANT PROTEIN / cyclic peptides / cyclotides / quasi-racemic
Function / homology
Function and homology information


defense response / killing of cells of another organism
Similarity search - Function
Cyclotide, bracelet, conserved site / Cyclotides bracelet subfamily signature. / Cyclotides profile. / Cyclotide / Cyclotide superfamily / Cyclotide family
Similarity search - Domain/homology
THIOCYANATE ION / polypeptide(D) / polypeptide(D) (> 10) / Cycloviolacin-O2
Similarity search - Component
Biological speciesViola odorata (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å
AuthorsHuang, Y.H. / Du, Q. / Craik, D.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Science and Industry Endowment Fund (SIEF)CE200100012 Australia
CitationJournal: 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
DepositionJul 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 13, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: [I11L]cycloviolacin O2
B: D-[I11L]cycloviolacin O2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4504
Polymers6,3342
Non-polymers1162
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-10 kcal/mol
Surface area4140 Å2
Unit cell
Length a, b, c (Å)27.095, 24.757, 30.244
Angle α, β, γ (deg.)90.00, 115.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide [I11L]cycloviolacin O2


Mass: 3167.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Viola odorata (plant) / References: UniProt: P58434
#2: Polypeptide(D) D-[I11L]cycloviolacin O2


Mass: 3165.756 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Viola odorata (plant) / References: UniProt: P58434
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Compound detailsThe authors state that chain B is indeed D-peptide and is all-D amino acids.
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 15.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium thiocyanate, 23% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.04→24.51 Å / Num. obs: 17453 / % possible obs: 98.98 % / Redundancy: 1.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.0396 / Net I/σ(I): 6.47
Reflection shellResolution: 1.04→1.077 Å / Num. unique obs: 1715 / CC1/2: 0.912

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2KNM

2knm


Resolution: 1.04→24.51 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1973 1740 9.97 %
Rwork0.1782 --
obs0.18 17452 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.04→24.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms430 0 6 40 476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014442
X-RAY DIFFRACTIONf_angle_d1.596592
X-RAY DIFFRACTIONf_dihedral_angle_d10.158110
X-RAY DIFFRACTIONf_chiral_restr0.10866
X-RAY DIFFRACTIONf_plane_restr0.00872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.04-1.070.26641380.22631194X-RAY DIFFRACTION91
1.07-1.10.24451390.18621305X-RAY DIFFRACTION99
1.1-1.140.19831420.16511307X-RAY DIFFRACTION99
1.14-1.190.17461510.16351326X-RAY DIFFRACTION100
1.19-1.240.19431440.15451303X-RAY DIFFRACTION99
1.24-1.310.2081440.15711328X-RAY DIFFRACTION100
1.31-1.390.16471490.16671311X-RAY DIFFRACTION100
1.39-1.50.19171470.15971310X-RAY DIFFRACTION99
1.5-1.650.19091450.16521335X-RAY DIFFRACTION99
1.65-1.890.17741460.17441332X-RAY DIFFRACTION99
1.89-2.370.18531480.18821309X-RAY DIFFRACTION98
2.38-24.510.21411470.19171352X-RAY DIFFRACTION97

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