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- PDB-4x9z: Dimeric conotoxin alphaD-GeXXA -

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Basic information

Entry
Database: PDB / ID: 4x9z
TitleDimeric conotoxin alphaD-GeXXA
ComponentsalphaD-conotoxin GeXXA from the venom of Conus generalis
KeywordsTOXIN / alpha-conotoxin / GeXXA / Nicotinic acetylcholine receptor / homodimer
Function / homologyhost cell postsynaptic membrane / acetylcholine receptor inhibitor activity / toxin activity / extracellular region / Alpha-conotoxin GeXXA
Function and homology information
Biological speciesConus generalis (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / AB_INITIO / Resolution: 1.5 Å
AuthorsXu, S. / Zhang, T. / Kompella, S. / Adams, D. / Ding, J. / Wang, C.
CitationJournal: Sci Rep / Year: 2015
Title: Conotoxin alpha D-GeXXA utilizes a novel strategy to antagonize nicotinic acetylcholine receptors
Authors: Xu, S. / Zhang, T. / Kompella, S.N. / Yan, M. / Lu, A. / Wang, Y. / Shao, X. / Chi, C. / Adams, D.J. / Ding, J. / Wang, C.
History
DepositionDec 12, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: alphaD-conotoxin GeXXA from the venom of Conus generalis
B: alphaD-conotoxin GeXXA from the venom of Conus generalis


Theoretical massNumber of molelcules
Total (without water)11,2892
Polymers11,2892
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-19 kcal/mol
Surface area6950 Å2
Unit cell
Length a, b, c (Å)25.436, 42.423, 83.013
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein/peptide alphaD-conotoxin GeXXA from the venom of Conus generalis


Mass: 5644.727 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: venom / Source: (natural) Conus generalis (invertebrata) / References: UniProt: A0A0A0VBX4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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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: 2.02 Å3/Da / Density % sol: 39.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1M citrate acid, 10% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 13989 / % possible obs: 92.8 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 47.5
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 4.6 / % possible all: 94.4

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Phasing

PhasingMethod: AB_INITIO

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
ACORNphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.5→41.51 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.454 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 709 5.1 %RANDOM
Rwork0.177 13236 --
obs0.1791 13236 92.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 128.71 Å2 / Biso mean: 40.899 Å2 / Biso min: 16.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2--1.57 Å20 Å2
3----2.14 Å2
Refinement stepCycle: final / Resolution: 1.5→41.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms715 0 0 69 784
Biso mean---47.63 -
Num. residues----95
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.019751
X-RAY DIFFRACTIONr_angle_refined_deg1.2771.9131017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.864594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.59517.03727
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.2115122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8461512
X-RAY DIFFRACTIONr_chiral_restr0.0810.2107
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021550
X-RAY DIFFRACTIONr_rigid_bond_restr2.6783751
X-RAY DIFFRACTIONr_sphericity_free32.967527
X-RAY DIFFRACTIONr_sphericity_bonded31.1635767
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 44 -
Rwork0.22 860 -
all-904 -
obs--93.2 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.44860.0219-0.21590.0787-0.00250.3857-0.0215-0.0043-0.0278-0.021-0.0082-0.00730.0467-0.03830.02980.02970.0072-0.00260.0124-0.0070.0222-1.2856-8.243726.7885
20.1591-0.1310.20221.2544-0.67060.58050.0033-0.0656-0.00730.10380.02090.0568-0.0825-0.0022-0.02420.0432-0.0127-0.00410.0868-0.0030.0255-7.7505-5.77196.1022
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 50
2X-RAY DIFFRACTION2B3 - 50

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