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- PDB-7ulr: recombinant kappa-bungarotoxin -

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Basic information

Entry
Database: PDB / ID: 7ulr
Titlerecombinant kappa-bungarotoxin
ComponentsKappa-bungarotoxin
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 toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / Snake toxin-like superfamily
Similarity search - Domain/homology
Biological speciesBungarus multicinctus (many-banded krait)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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 kappa-bungarotoxin at 1.8 Angstroms resolution.
Authors: Xu, J. / Lei, X. / Chen, L.
History
DepositionApr 5, 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kappa-bungarotoxin
B: Kappa-bungarotoxin


Theoretical massNumber of molelcules
Total (without water)14,8272
Polymers14,8272
Non-polymers00
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-6 kcal/mol
Surface area8060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.090, 30.990, 39.430
Angle α, β, γ (deg.)70.440, 75.970, 71.940
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 16 or resid 18...
d_2ens_1(chain "B" and (resid 2 through 16 or resid 18...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ARGARGPROPROAA2 - 162 - 16
d_12GLYGLYLYSLYSAA18 - 3018 - 30
d_13CYSCYSSERSERAA32 - 3332 - 33
d_14GLYGLYTYRTYRAA36 - 5436 - 54
d_15SERSERHISHISAA56 - 6756 - 67
d_21ARGARGPROPROBB2 - 162 - 16
d_22GLYGLYLYSLYSBB18 - 3018 - 30
d_23CYSCYSSERSERBB32 - 3332 - 33
d_24GLYGLYTYRTYRBB36 - 5436 - 54
d_25SERSERHISHISBB56 - 6756 - 67

NCS oper: (Code: givenMatrix: (0.587694993783, 0.666264657981, 0.459027232098), (0.673119754988, -0.717416186923, 0.17950991668), (0.448914679787, 0.203483218636, -0.87009780485)Vector: 7. ...NCS oper: (Code: given
Matrix: (0.587694993783, 0.666264657981, 0.459027232098), (0.673119754988, -0.717416186923, 0.17950991668), (0.448914679787, 0.203483218636, -0.87009780485)
Vector: 7.37827888574, -3.9776115974, -20.2002997055)

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Components

#1: Protein Kappa-bungarotoxin / Kappa-bgt / Kappa-1-bungarotoxin / Long neurotoxin 2 / Neuronal bungarotoxin / nBgt / Toxin F


Mass: 7413.546 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bungarus multicinctus (many-banded krait)
Production host: Escherichia coli (E. coli) / References: UniProt: P01398
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 1.94 Å3/Da / Density % sol: 36.8 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 117 mg/ml in 200 mM NH4Ac, pH 7.0, 1:1 with 0.15 M DL-malic acid pH 7.0, 20% PEG 3350 at 4 degree centigrade

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.77→36.71 Å / Num. obs: 19608 / % possible obs: 93 % / Redundancy: 4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.047 / Rrim(I) all: 0.067 / Net I/σ(I): 13.5
Reflection shellResolution: 1.77→1.81 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.092 / Mean I/σ(I) obs: 8.6 / Num. unique obs: 574 / CC1/2: 0.983 / Rpim(I) all: 0.092 / Rrim(I) all: 0.13 / % possible all: 86.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KBA

1kba


Resolution: 1.8→36.71 Å / SU ML: 0.1471 / Cross valid method: FREE R-VALUE / σ(F): 2.05 / Phase error: 20.5678
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1901 1006 5.13 %
Rwork0.1653 18596 -
obs0.1666 19602 93.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.55 Å2
Refinement stepCycle: LAST / Resolution: 1.8→36.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1018 0 0 160 1178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00691036
X-RAY DIFFRACTIONf_angle_d1.00821404
X-RAY DIFFRACTIONf_chiral_restr0.0564160
X-RAY DIFFRACTIONf_plane_restr0.0102188
X-RAY DIFFRACTIONf_dihedral_angle_d16.2489392
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.14223440479 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.890.20061480.19692517X-RAY DIFFRACTION89.79
1.89-2.010.19921280.16562588X-RAY DIFFRACTION91.57
2.01-2.170.17561360.16112637X-RAY DIFFRACTION91.88
2.17-2.390.21121640.172639X-RAY DIFFRACTION93.12
2.39-2.730.18881390.17822709X-RAY DIFFRACTION94.3
2.73-3.440.17181500.1752732X-RAY DIFFRACTION95.43
3.44-36.710.19651410.1452774X-RAY DIFFRACTION97.36
Refinement TLS params.Method: refined / Origin x: 0.793520574425 Å / Origin y: -3.23208132999 Å / Origin z: -10.9890284254 Å
111213212223313233
T0.0720545319483 Å20.000311405656763 Å20.00118045836134 Å2-0.0526466030608 Å20.00369817518449 Å2--0.0357954355758 Å2
L0.48914815974 °20.215188658333 °2-0.0446665606378 °2-0.419228106256 °2-0.102348548972 °2--0.377110355559 °2
S-0.0431493185186 Å °0.0722880686899 Å °0.0732188522853 Å °-0.216902883827 Å °-0.024774314649 Å °-0.0944612718423 Å °0.0817819425746 Å °-0.0121078146936 Å °-0.0039181793137 Å °
Refinement TLS groupSelection details: all

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