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- PDB-6atm: Exploring Cystine Dense Peptide Space to Open a Unique Molecular ... -

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Basic information

Entry
Database: PDB / ID: 6atm
TitleExploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox
ComponentsPotassium channel toxin alpha-KTx 3.10
KeywordsTOXIN / Knottins / Cystine knot / Toxins
Function / homologyScorpion short toxins signature. / Scorpion short chain toxin, potassium channel inhibitor / Scorpion short toxin, BmKK2 / Knottin, scorpion toxin-like superfamily / ion channel inhibitor activity / potassium channel regulator activity / toxin activity / extracellular region / Potassium channel toxin alpha-KTx 3.10
Function and homology information
Biological speciesButhus occitanus israelis (scorpion)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsGewe, M.M. / Rupert, P. / Strong, R.K.
CitationJournal: To Be Published
Title: Exploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox
Authors: Correnti, C. / Gewe, M.M.
History
DepositionAug 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Potassium channel toxin alpha-KTx 3.10


Theoretical massNumber of molelcules
Total (without water)4,1771
Polymers4,1771
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.831, 50.750, 27.657
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-124-

HOH

21C-127-

HOH

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Components

#1: Protein/peptide Potassium channel toxin alpha-KTx 3.10 / BoiTx1


Mass: 4177.003 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Buthus occitanus israelis (scorpion) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P0C908
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 1.84 Å3/Da / Density % sol: 33.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.2 / Details: 1.6M tri-Na Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 23, 2016
RadiationMonochromator: osmic varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 6993 / % possible obs: 99 % / Redundancy: 3.7 % / Net I/σ(I): 51.05
Reflection shellResolution: 2.09→2.13 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.04 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 289 / CC1/2: 0.995 / Rpim(I) all: 0.028 / Rsym value: 0.05 / % possible all: 89.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000708cdata reduction
HKL-2000708cdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→33.17 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.738 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.161 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23571 138 5.2 %RANDOM
Rwork0.1524 ---
obs0.1565 2509 86.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.09→33.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms285 0 0 33 318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.019292
X-RAY DIFFRACTIONr_bond_other_d0.0020.02280
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.993390
X-RAY DIFFRACTIONr_angle_other_deg0.8593657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.778538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.46421.1119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.6691556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.358153
X-RAY DIFFRACTIONr_chiral_restr0.090.240
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021317
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0254
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.082.876155
X-RAY DIFFRACTIONr_mcbond_other3.0792.877154
X-RAY DIFFRACTIONr_mcangle_it4.6674.764192
X-RAY DIFFRACTIONr_mcangle_other4.6584.766193
X-RAY DIFFRACTIONr_scbond_it4.4433.352137
X-RAY DIFFRACTIONr_scbond_other4.4073.353137
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.375.264198
X-RAY DIFFRACTIONr_long_range_B_refined8.04626.208309
X-RAY DIFFRACTIONr_long_range_B_other8.04725.907305
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 5 -
Rwork0.305 59 -
obs--28.32 %

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