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- PDB-7rih: hyen D -

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Basic information

Entry
Database: PDB / ID: 7rih
Titlehyen D
Components
  • Cyclotide hyen-D
  • D-[I11L]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
CITRATE ANION / polypeptide(D) / polypeptide(D) (> 10) / Cyclotide hyen-D
Similarity search - Component
Biological speciesHybanthus enneaspermus (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 22, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 9, 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: D-[I11L]hyen D
B: Cyclotide hyen-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7414
Polymers6,3632
Non-polymers3782
Water1,44180
1
A: D-[I11L]hyen D
hetero molecules

B: Cyclotide hyen-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7414
Polymers6,3632
Non-polymers3782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y+1/2,-z1
Buried area1160 Å2
ΔGint-7 kcal/mol
Surface area4230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.038, 24.731, 34.729
Angle α, β, γ (deg.)90.000, 102.470, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Polypeptide(D) D-[I11L]hyen D


Mass: 3179.757 Da / Num. of mol.: 1 / Mutation: I11L / Source method: obtained synthetically / Source: (synth.) Hybanthus enneaspermus (plant)
#2: Protein/peptide Cyclotide hyen-D


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 ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
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: 1.72 Å3/Da / Density % sol: 28.32 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95366 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: 0.95366 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.35→1.39 Å / Num. unique obs: 507 / CC1/2: 0.998

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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: 7RII

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
RfactorNum. reflection% reflection
Rfree0.2154 910 10.02 %
Rwork0.1808 8171 -
obs0.1842 9077 93.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 36.84 Å2 / Biso mean: 13.5378 Å2 / Biso min: 6.48 Å2
Refinement stepCycle: final / Resolution: 1.35→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms434 0 36 80 550
Biso mean--18.16 21.91 -
Num. residues----60
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor Rfree error% reflection obs (%)
1.35-1.420.29341270.24251120091
1.42-1.510.26941260.22371147093
1.51-1.630.25171310.19351183095
1.63-1.790.21121310.18121175096
1.79-2.050.19571310.17761178095
2.05-2.580.21981270.18081150092
2.58-19.980.19311370.16151218095
Refinement TLS params.Method: refined / Origin x: -6.3242 Å / Origin y: -5.9358 Å / Origin z: 2.5514 Å
111213212223313233
T0.0775 Å20.0062 Å2-0.0173 Å2-0.0684 Å2-0.0021 Å2--0.1006 Å2
L0.066 °20.034 °2-0.0102 °2-0.362 °2-0.234 °2--0.7509 °2
S-0.0294 Å °-0.0325 Å °0.053 Å °0.0678 Å °0.0069 Å °-0.0803 Å °0.0259 Å °0.0451 Å °0.0126 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 30
2X-RAY DIFFRACTION1allA101
3X-RAY DIFFRACTION1allB1 - 30
4X-RAY DIFFRACTION1allB101
5X-RAY DIFFRACTION1allS1 - 80

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