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- PDB-3e4h: Crystal structure of the cyclotide varv F -

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Basic information

Entry
Database: PDB / ID: 3e4h
TitleCrystal structure of the cyclotide varv F
ComponentsVarv peptide F,Varv peptide F
KeywordsPLANT PROTEIN / cyclotide / circular proteins / cystine knot / cyclization / Knottin / Plant defense
Function / homologyCyclotide, moebius, conserved site / Cyclotides Moebius subfamily signature. / Cyclotides profile. / Cyclotide / Cyclotide superfamily / Cyclotide family / defense response / Varv peptide F
Function and homology information
Biological speciesViola arvensis (European field pansy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHu, S.H.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Combined X-ray and NMR Analysis of the Stability of the Cyclotide Cystine Knot Fold That Underpins Its Insecticidal Activity and Potential Use as a Drug Scaffold
Authors: Wang, C.K. / Hu, S.H. / Martin, J.L. / Hajdu, J. / Bohlin, L. / Claeson, P. / Rosengren, K.J. / Tang, J. / Tan, N.H. / Craik, D.J.
History
DepositionAug 11, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Varv peptide F,Varv peptide F


Theoretical massNumber of molelcules
Total (without water)2,9841
Polymers2,9841
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Varv peptide F,Varv peptide F
x 6


Theoretical massNumber of molelcules
Total (without water)17,9076
Polymers17,9076
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation38_555-y+1/4,-x+1/4,-z+1/41
crystal symmetry operation43_555-x+1/4,-z+1/4,-y+1/41
crystal symmetry operation48_555-z+1/4,-y+1/4,-x+1/41
Buried area3400 Å2
ΔGint-42.1 kcal/mol
Surface area9000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.081, 84.081, 84.081
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-68-

HOH

21A-70-

HOH

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Components

#1: Protein/peptide Varv peptide F,Varv peptide F


Mass: 2984.432 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Viola arvensis (European field pansy) / References: UniProt: P58451
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
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: 4.15 Å3/Da / Density % sol: 70.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 2.0M MgCl2, 0.1M bicine, pH9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.052 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 6, 2000 / Details: Osmic Max-Flux optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.052 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 4978 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 35.8 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.061
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 35.6 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 8.9 / Num. unique all: 479 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NB1

1nb1


Resolution: 1.8→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 264 -Random
Rwork0.224 ---
all-4973 --
obs-4863 97.8 %-
Displacement parametersBiso mean: 21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms202 0 0 45 247
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_torsion_deg27.5
X-RAY DIFFRACTIONc_improper_angle_d0
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.244 24 -
Rwork0.261 --
obs-427 94 %

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