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- PDB-7ulg: recombinant alpha cobra toxin -

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Basic information

Entry
Database: PDB / ID: 7ulg
Titlerecombinant alpha cobra toxin
ComponentsAlpha-cobratoxin
KeywordsBIOSYNTHETIC PROTEIN / recombinant / alpha neurotoxin / refolded
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / Snake toxin-like superfamily
Similarity search - Domain/homology
ACETATE ION / Alpha-cobratoxin
Similarity search - Component
Biological speciesNaja kaouthia (monocled cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsXu, J. / Lei, X. / Chen, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM064642 United States
CitationJournal: To Be Published
Title: Structure of recombinant alpha cobra toxin at 1.57 Angstroms
Authors: Xu, J. / Lei, X. / Chen, L.
History
DepositionApr 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-cobratoxin
B: Alpha-cobratoxin
C: Alpha-cobratoxin
D: Alpha-cobratoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1916
Polymers31,8934
Non-polymers2972
Water7,458414
1
A: Alpha-cobratoxin


Theoretical massNumber of molelcules
Total (without water)7,9731
Polymers7,9731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha-cobratoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2122
Polymers7,9731
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Alpha-cobratoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0322
Polymers7,9731
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Alpha-cobratoxin


Theoretical massNumber of molelcules
Total (without water)7,9731
Polymers7,9731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.969, 73.969, 110.841
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11B-268-

HOH

21B-294-

HOH

31B-297-

HOH

41C-271-

HOH

51C-300-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 1 and (name N or name...
d_2ens_1(chain "B" and ((resid 1 and (name N or name...
d_3ens_1(chain "C" and ((resid 1 and (name N or name...
d_4ens_1(chain "D" and ((resid 1 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ILELYSA2 - 13
d_12ens_1CYSLYSA15 - 50
d_13ens_1GLYTHRA52 - 68
d_21ens_1ILELYSB2 - 13
d_22ens_1CYSLYSB15 - 50
d_23ens_1GLYTHRB52 - 68
d_31ens_1ILELYSD2 - 13
d_32ens_1CYSLYSD15 - 50
d_33ens_1GLYTHRD52 - 68
d_41ens_1ILELYSF2 - 13
d_42ens_1CYSLYSF15 - 50
d_43ens_1GLYTHRF52 - 68

NCS oper:
IDCodeMatrixVector
1given(-0.30498743346, 0.199776260879, -0.931167069339), (0.768389697127, 0.629257976894, -0.116669069868), (0.562636595664, -0.751081782567, -0.345421795947)67.5286489132, -17.516426776, 30.2020013094
2given(-0.0143579295649, -0.325332551403, -0.945490656144), (-0.938402406625, 0.330878413385, -0.0996011987648), (0.345245960293, 0.885820640171, -0.310043578144)68.2851863432, 51.5996465851, 1.11094787862
3given(-0.00574683401775, -0.939112549556, 0.343561629356), (-0.351386655288, 0.323553885109, 0.878544422278), (-0.936212792256, -0.115674122853, -0.331851028201)48.8630106735, 5.50827592641, 71.2615921554

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Components

#1: Protein
Alpha-cobratoxin / Alpha-CT / Alpha-CbT / Alpha-Cbtx / Alpha-Ctx / Alpha-elapitoxin-Nk2a / Alpha-EPTX-Nk2a / Long ...Alpha-CT / Alpha-CbT / Alpha-Cbtx / Alpha-Ctx / Alpha-elapitoxin-Nk2a / Alpha-EPTX-Nk2a / Long neurotoxin 1 / Siamensis 3


Mass: 7973.290 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naja kaouthia (monocled cobra) / Production host: Escherichia coli (E. coli) / References: UniProt: P01391
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.74 Å3/Da / Density % sol: 55.19 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 110 mg/ml in 200 mM NH4Ac (pH 7.0/25 DC), 1:1 with 0.1 M HEPES (pH 7.9), 30% Jeffamine M-600 (pH 7.0), 18 DC
Temp details: 18 degree centigrade

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00007 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00007 Å / Relative weight: 1
ReflectionResolution: 1.57→64.06 Å / Num. obs: 94685 / % possible obs: 99.9 % / Redundancy: 21.7 % / Biso Wilson estimate: 20.76 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 21.8
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 19.7 % / Rmerge(I) obs: 0.904 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 2482 / CC1/2: 0.943 / Rpim(I) all: 0.211 / Rrim(I) all: 0.945 / % possible all: 99.79

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NTN,4LFT, 6ZFM, 1HC9

1ntn

4lft

6zfm

1hc9


Resolution: 1.57→41.91 Å / SU ML: 0.146 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.7686
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1812 4799 5.07 %
Rwork0.1691 89873 -
obs0.1697 94672 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.68 Å2
Refinement stepCycle: LAST / Resolution: 1.57→41.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 19 414 2473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01212102
X-RAY DIFFRACTIONf_angle_d1.25922859
X-RAY DIFFRACTIONf_chiral_restr0.0742332
X-RAY DIFFRACTIONf_plane_restr0.0136365
X-RAY DIFFRACTIONf_dihedral_angle_d11.623763
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.456157008963
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.298667814429
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.318846655331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.590.26391560.23612940X-RAY DIFFRACTION99.77
1.59-1.610.26061440.23983102X-RAY DIFFRACTION99.88
1.61-1.630.241400.22752955X-RAY DIFFRACTION99.97
1.63-1.650.23811280.22373063X-RAY DIFFRACTION99.84
1.65-1.670.21681500.20472932X-RAY DIFFRACTION99.9
1.67-1.690.21191600.1983031X-RAY DIFFRACTION99.91
1.69-1.720.20761800.19422978X-RAY DIFFRACTION99.97
1.72-1.740.19961300.1933007X-RAY DIFFRACTION99.97
1.74-1.770.2342060.20742960X-RAY DIFFRACTION99.97
1.77-1.80.21941480.19553013X-RAY DIFFRACTION99.91
1.8-1.830.20721440.18693052X-RAY DIFFRACTION99.97
1.83-1.860.16121470.18682989X-RAY DIFFRACTION100
1.86-1.90.19191760.17612994X-RAY DIFFRACTION100
1.9-1.940.17331760.17262975X-RAY DIFFRACTION100
1.94-1.980.181580.16452986X-RAY DIFFRACTION100
1.98-2.020.16061580.16442991X-RAY DIFFRACTION100
2.02-2.070.16011820.15672954X-RAY DIFFRACTION100
2.07-2.130.16371660.16243041X-RAY DIFFRACTION100
2.13-2.190.18851260.163014X-RAY DIFFRACTION99.97
2.19-2.260.16141680.1522959X-RAY DIFFRACTION100
2.26-2.350.19231580.1643031X-RAY DIFFRACTION99.97
2.35-2.440.17971300.16783017X-RAY DIFFRACTION100
2.44-2.550.17611610.16983036X-RAY DIFFRACTION100
2.55-2.680.18911790.16522965X-RAY DIFFRACTION100
2.68-2.850.20461660.17853024X-RAY DIFFRACTION100
2.85-3.070.17281670.15622993X-RAY DIFFRACTION100
3.07-3.380.15361620.15622974X-RAY DIFFRACTION100
3.38-3.870.18551730.16122999X-RAY DIFFRACTION100
3.87-4.880.16471590.14652989X-RAY DIFFRACTION99.9
4.88-41.910.18252010.18722909X-RAY DIFFRACTION97.55

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