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- PDB-4ttl: Racemic structure of cyclic Vc1.1 (cVc1.1-1) -

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Basic information

Entry
Database: PDB / ID: 4ttl
TitleRacemic structure of cyclic Vc1.1 (cVc1.1-1)
ComponentsAlpha-conotoxin Vc1A
KeywordsTOXIN / cyclic peptide / disulfide bond
Function / homology
Function and homology information


host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Conotoxin, alpha-type / Alpha conotoxin precursor / Conotoxin, alpha-type, conserved site / Alpha-conotoxin family signature.
Similarity search - Domain/homology
Alpha-conotoxin Vc1a
Similarity search - Component
Biological speciesConus victoriae (invertebrata)
MethodX-RAY DIFFRACTION / Resolution: 1.7004 Å
AuthorsWang, C.K. / King, G.J. / Craik, D.J.
Funding support Australia, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)LP110200213 Australia
National Health and Medical Research Council (NHMRC, Australia)546578 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1026501 Australia
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Racemic and Quasi-Racemic X-ray Structures of Cyclic Disulfide-Rich Peptide Drug Scaffolds.
Authors: Wang, C.K. / King, G.J. / Northfield, S.E. / Ojeda, P.G. / Craik, D.J.
History
DepositionJun 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Jul 20, 2016Group: Data collection
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn
Item: _pdbx_audit_support.funding_organization / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-conotoxin Vc1A


Theoretical massNumber of molelcules
Total (without water)2,1841
Polymers2,1841
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.256, 20.706, 38.236
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number61
Space group name H-MPbca
DetailsCrystal obtained from racemic mixture of D- and L- enantiomers of SFTI-1. The D-form is represented in the asymmetric unit.

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Components

#1: Protein/peptide Alpha-conotoxin Vc1A / Alpha-Vc1A / Vc1.1


Mass: 2184.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Conus victoriae (invertebrata) / References: UniProt: P69747
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.0 M HEPES pH 7.5, 0.86 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→19.12 Å / Num. obs: 2551 / % possible obs: 100 % / Redundancy: 6.73 % / Biso Wilson estimate: 49.14 Å2 / Net I/σ(I): 11.6
Reflection shellResolution: 1.7→1.76 Å / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.391 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
CrystalCleardata reduction
PDB_EXTRACT3.14data extraction
SCALEPACKdata scaling
RefinementResolution: 1.7004→19.118 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 22.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2259 255 10.02 %
Rwork0.1887 --
obs0.1931 2546 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: final / Resolution: 1.7004→19.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms148 0 0 21 169
Biso mean---31.24 -
Num. residues----22
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007171
X-RAY DIFFRACTIONf_angle_d1.101231
X-RAY DIFFRACTIONf_dihedral_angle_d11.3964
X-RAY DIFFRACTIONf_chiral_restr0.05121
X-RAY DIFFRACTIONf_plane_restr0.00535
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7004-2.14190.28451270.22791146X-RAY DIFFRACTION100
2.1419-19.11930.20731280.17591145X-RAY DIFFRACTION100

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