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- PDB-7rii: [I11L]hyen D crystal structure -

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Basic information

Entry
Database: PDB / ID: 7rii
Title[I11L]hyen D crystal structure
ComponentsCyclotide hyen-D
KeywordsPLANT 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
Cyclotide, bracelet, conserved site / Cyclotides bracelet subfamily signature. / Cyclotides profile. / Cyclotide / Cyclotide superfamily / Cyclotide family
Similarity search - Domain/homology
PHOSPHATE ION / Cyclotide hyen-D
Similarity search - Component
Biological speciesHybanthus enneaspermus (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsDu, Q. / Huang, Y.H. / Craik, D.J. / Wang, C.K.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)CE200100012 Australia
CitationJournal: 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
DepositionJul 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclotide hyen-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,2782
Polymers3,1831
Non-polymers951
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)18.755, 21.153, 26.296
Angle α, β, γ (deg.)87.250, 82.940, 89.130
Int Tables number2
Space group name H-MP-1

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Components

#1: Protein/peptide Cyclotide hyen-D


Mass: 3182.778 Da / Num. of mol.: 1 / Mutation: I11L / Source method: obtained synthetically / Source: (synth.) Hybanthus enneaspermus (plant) / References: UniProt: C0HLN8
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.62 Å3/Da / Density % sol: 24.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.22→21.13 Å / Num. obs: 11130 / % possible obs: 93.26 % / Redundancy: 3.4 % / CC1/2: 0.989 / Rmerge(I) obs: 0.1293 / Net I/σ(I): 5.09
Reflection shellResolution: 1.22→1.264 Å / Num. unique obs: 1091 / CC1/2: 0.889

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2KNM

2knm


Resolution: 1.22→21.13 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 16.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2233 1111 9.99 %
Rwork0.2047 10013 -
obs0.2065 11124 93.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 34.99 Å2 / Biso mean: 9.7245 Å2 / Biso min: 5.7 Å2
Refinement stepCycle: final / Resolution: 1.22→21.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms217 0 5 32 254
Biso mean--11.63 17.13 -
Num. residues----30
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.22-1.280.36111320.32111216134891
1.28-1.340.39891430.30121227137091
1.34-1.430.28761340.25481241137593
1.43-1.540.25281360.21791244138093
1.54-1.690.2071450.19911253139894
1.69-1.940.16921370.17621272140994
1.94-2.440.19351430.17571277142096
2.44-21.130.19731410.18461283142495
Refinement TLS params.Method: refined / Origin x: 7.2404 Å / Origin y: 3.5327 Å / Origin z: 5.8203 Å
111213212223313233
T0.0702 Å2-0.0059 Å2-0.0014 Å2-0.0877 Å2-0.0081 Å2--0.0585 Å2
L0.6598 °2-0.0073 °20.2318 °2-1.6521 °2-1.1163 °2--1.231 °2
S0.0315 Å °0.0403 Å °0.01 Å °-0.0152 Å °-0.0148 Å °0.0403 Å °0.0095 Å °0.014 Å °-0.0196 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 30
2X-RAY DIFFRACTION1allA101
3X-RAY DIFFRACTION1allS1 - 36

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