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- PDB-4u5h: crystal structure of con-ikot-ikot toxin -

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Basic information

Entry
Database: PDB / ID: 4u5h
Titlecrystal structure of con-ikot-ikot toxin
ComponentsCon-ikot-ikot
KeywordsTOXIN
Function / homology
Function and homology information


host cell postsynaptic membrane / ion channel regulator activity / toxin activity / extracellular region / identical protein binding
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1800 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesConus striatus (striated cone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.58 Å
AuthorsChen, L. / Gouaux, E.
CitationJournal: Science / Year: 2014
Title: X-ray structures of AMPA receptor-cone snail toxin complexes illuminate activation mechanism.
Authors: Chen, L. / Durr, K.L. / Gouaux, E.
History
DepositionJul 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Con-ikot-ikot
B: Con-ikot-ikot
C: Con-ikot-ikot
D: Con-ikot-ikot
E: Con-ikot-ikot
F: Con-ikot-ikot
G: Con-ikot-ikot
H: Con-ikot-ikot


Theoretical massNumber of molelcules
Total (without water)78,0258
Polymers78,0258
Non-polymers00
Water11,349630
1
C: Con-ikot-ikot
D: Con-ikot-ikot


Theoretical massNumber of molelcules
Total (without water)19,5062
Polymers19,5062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-15 kcal/mol
Surface area8710 Å2
MethodPISA
2
E: Con-ikot-ikot
F: Con-ikot-ikot


Theoretical massNumber of molelcules
Total (without water)19,5062
Polymers19,5062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-15 kcal/mol
Surface area8720 Å2
MethodPISA
3
G: Con-ikot-ikot
H: Con-ikot-ikot


Theoretical massNumber of molelcules
Total (without water)19,5062
Polymers19,5062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-15 kcal/mol
Surface area9380 Å2
MethodPISA
4
A: Con-ikot-ikot
B: Con-ikot-ikot


Theoretical massNumber of molelcules
Total (without water)19,5062
Polymers19,5062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-14 kcal/mol
Surface area8840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.910, 144.860, 48.600
Angle α, β, γ (deg.)90.000, 94.630, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F
71chain G
81chain H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ALA / End label comp-ID: ALA

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLYGLYchain AAA2 - 866 - 90
2SERSERchain BBB0 - 864 - 90
3PROPROchain CCC3 - 867 - 90
4GLYGLYchain DDD2 - 866 - 90
5GLYGLYchain EEE2 - 866 - 90
6GLYGLYchain FFF2 - 866 - 90
7GLYGLYchain GGG-3 - 861 - 90
8SERSERchain HHH1 - 865 - 90

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Components

#1: Protein
Con-ikot-ikot


Mass: 9753.155 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Conus striatus (striated cone) / Production host: Escherichia coli (E. coli) / References: UniProt: P0CB20
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 630 / 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

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris pH 8.5, 35% methanol, 16% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→42.77 Å / Num. obs: 80044 / % possible obs: 99.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 13.03 Å2 / Net I/σ(I): 9.3
Reflection shellResolution: 1.58→1.62 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.4 / % possible all: 99.5

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Processing

Software
NameVersionClassification
XDSdata scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.2_1309)refinement
RefinementResolution: 1.58→19.903 Å / FOM work R set: 0.8603 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2112 4010 5.02 %
Rwork0.1937 75945 -
obs0.1946 79955 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.08 Å2 / Biso mean: 15.71 Å2 / Biso min: 4.35 Å2
Refinement stepCycle: final / Resolution: 1.58→19.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5169 0 0 630 5799
Biso mean---24.77 -
Num. residues----687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055302
X-RAY DIFFRACTIONf_angle_d1.0667056
X-RAY DIFFRACTIONf_chiral_restr0.053750
X-RAY DIFFRACTIONf_plane_restr0.004943
X-RAY DIFFRACTIONf_dihedral_angle_d11.241959
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3189X-RAY DIFFRACTION13.936TORSIONAL
12B3189X-RAY DIFFRACTION13.936TORSIONAL
13C3189X-RAY DIFFRACTION13.936TORSIONAL
14D3189X-RAY DIFFRACTION13.936TORSIONAL
15E3189X-RAY DIFFRACTION13.936TORSIONAL
16F3189X-RAY DIFFRACTION13.936TORSIONAL
17G3189X-RAY DIFFRACTION13.936TORSIONAL
18H3189X-RAY DIFFRACTION13.936TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.58-1.59860.28631430.255725942737100
1.5986-1.61810.26881460.23572637278399
1.6181-1.63860.24011420.22952600274299
1.6386-1.66010.26111520.22042609276199
1.6601-1.68280.28551320.23412628276099
1.6828-1.70690.26811200.221525852705100
1.7069-1.73230.27741380.23182689282799
1.7323-1.75940.26441260.22852562268899
1.7594-1.78820.24771300.21962676280699
1.7882-1.8190.20011340.21732579271399
1.819-1.85210.24621350.214426362771100
1.8521-1.88770.24711250.21122638276399
1.8877-1.92620.26581360.20392613274999
1.9262-1.9680.22061400.19622621276199
1.968-2.01380.2451440.20272616276099
2.0138-2.06410.24831250.199326482773100
2.0641-2.11980.20851350.19032601273699
2.1198-2.18210.20861460.18382593273999
2.1821-2.25250.19261480.18062619276799
2.2525-2.33280.21211530.17912602275599
2.3328-2.42610.19391350.18232627276299
2.4261-2.53630.19321320.18362618275099
2.5363-2.66970.19271570.184226222779100
2.6697-2.83650.20951540.1862597275199
2.8365-3.05480.21271260.1832655278199
3.0548-3.36090.18551440.19012598274299
3.3609-3.84420.19351280.17452621274999
3.8442-4.83180.17611420.17722630277298
4.8318-19.9050.18531420.19722631277399

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